ENST00000445560:c.-192G>C

Variant names:

• chr11-66002338-G-C
• rs1786171
• ENST00000445560.6:c.-192G>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000445560.6(BANF1):​c.-192G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 152,270 control chromosomes in the GnomAD database, including 39,875 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.71 (39858 hom., cov: 34)
  • Exomes 𝑓: 0.80 (17 hom.)
• Consequence: BANF1 ENST00000445560.6 5_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0630
• Publications: 5 publications found

Genes affected

BANF1 (HGNC:17397): (BAF nuclear assembly factor 1) The protein encoded by this gene was first identified by its ability to protect retroviruses from intramolecular integration and therefore promote intermolecular integration into the host cell genome. The protein forms a homodimer which localizes to both the nucleus and cytoplasm and is specifically associated with chromosomes during mitosis. This protein binds to double stranded DNA in a non-specific manner and also binds to LEM-domain containing proteins of the nuclear envelope. This protein is thought to facilitate nuclear reassembly by binding with both DNA and inner nuclear membrane proteins and thereby recruit chromatin to the nuclear periphery. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Jan 2009]

EIF1AD (HGNC:28147): (eukaryotic translation initiation factor 1A domain containing) Predicted to enable translation initiation factor activity. Predicted to be involved in translational initiation. Located in intermediate filament cytoskeleton and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 11-66002338-G-C is Benign according to our data. Variant chr11-66002338-G-C is described in ClinVar as Benign. ClinVar VariationId is 305401.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445560.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	EIF1AD	NM_001242481.2	MANE Select	c.-545C>G		upstream_gene	N/A	NP_001229410.1	Q8N9N8
	BANF1	NM_003860.4	MANE Select	c.-249G>C		upstream_gene	N/A	NP_003851.1	O75531
	EIF1AD	NM_001242482.2		c.-521C>G		upstream_gene	N/A	NP_001229411.1	Q8N9N8

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANF1	ENST00000445560.6	TSL:1	c.-192G>C		5_prime_UTR	Exon 1 of 3	ENSP00000416128.2	O75531
	EIF1AD	ENST00000935685.1		c.-626C>G		5_prime_UTR	Exon 1 of 6	ENSP00000605744.1
	EIF1AD	ENST00000949577.1		c.-128C>G		5_prime_UTR	Exon 1 of 7	ENSP00000619636.1

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107793 AN: 152106 Hom.: 39849 Cov.: 34

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.871

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.799

Gnomad OTH AF: 0.703

GnomAD4 exome AF: 0.804 AC: 37 AN: 46 Hom.: 17 Cov.: 0 AF XY: 0.853 AC XY: 29 AN XY: 34

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 6 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.735 AC: 25 AN: 34

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.708 AC: 107836 AN: 152224 Hom.: 39858 Cov.: 34 AF XY: 0.716 AC XY: 53279 AN XY: 74438

African (AFR) AF: 0.475 AC: 19712 AN: 41508

American (AMR) AF: 0.802 AC: 12268 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.745 AC: 2584 AN: 3468

East Asian (EAS) AF: 0.685 AC: 3541 AN: 5168

South Asian (SAS) AF: 0.778 AC: 3750 AN: 4822

European-Finnish (FIN) AF: 0.871 AC: 9248 AN: 10616

Middle Eastern (MID) AF: 0.786 AC: 231 AN: 294

European-Non Finnish (NFE) AF: 0.799 AC: 54382 AN: 68022

Other (OTH) AF: 0.707 AC: 1494 AN: 2114

Alfa AF: 0.762 Hom.: 5642

Bravo AF: 0.692

Asia WGS AF: 0.743 AC: 2582 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	1	Nestor-Guillermo progeria syndrome (1)
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.8
DANN	Benign	0.79
PhyloP100		-0.063
PromoterAI		-0.023	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Mutation Taster		=300/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1786171; hg19: chr11-65769809;