chr11-66003872-C-T

Variant names:

• chr11-66003872-C-T
• rs145574018
• NM_003860.4:c.*100C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Strong BP6_Moderate BS2

The NM_003860.4(BANF1):​c.*100C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000753 in 1,549,076 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0039 (3 hom., cov: 31)
  • Exomes 𝑓: 0.00041 (9 hom.)
• Consequence: BANF1 NM_003860.4 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.304
• Publications: 0 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]

BANF1 Gene-Disease associations (from GenCC):

• Nestor-Guillermo progeria syndrome

  Inheritance: AR, Unknown Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Orphanet, ClinGen, Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BP6: Variant 11-66003872-C-T is Benign according to our data. Variant chr11-66003872-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 877794.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 3 AR,Unknown gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003860.4. 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
	BANF1	NM_003860.4	MANE Select	c.*100C>T		3_prime_UTR	Exon 3 of 3	NP_003851.1	O75531
	BANF1	NM_001143985.2		c.*100C>T		3_prime_UTR	Exon 3 of 3	NP_001137457.1
	BANF1	NM_001440618.1		c.*100C>T		3_prime_UTR	Exon 3 of 3	NP_001427547.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BANF1	ENST00000312175.7	TSL:1 MANE Select	c.*100C>T		3_prime_UTR	Exon 3 of 3	ENSP00000310275.2	O75531
	BANF1	ENST00000445560.6	TSL:1	c.*100C>T		3_prime_UTR	Exon 3 of 3	ENSP00000416128.2	O75531
	BANF1	ENST00000527348.1	TSL:3	c.*100C>T		3_prime_UTR	Exon 3 of 3	ENSP00000432867.1	O75531

Frequencies

GnomAD3 genomes AF: 0.00386 AC: 587 AN: 152118 Hom.: 3 Cov.: 31

Gnomad AFR AF: 0.0134

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00118

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00528

GnomAD4 exome AF: 0.000414 AC: 578 AN: 1396840 Hom.: 9 Cov.: 23 AF XY: 0.000363 AC XY: 253 AN XY: 696548

African (AFR) AF: 0.0146 AC: 468 AN: 31950

American (AMR) AF: 0.000613 AC: 26 AN: 42438

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25454

East Asian (EAS) AF: 0.00 AC: 0 AN: 38774

South Asian (SAS) AF: 0.000132 AC: 11 AN: 83060

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 49210

Middle Eastern (MID) AF: 0.000478 AC: 2 AN: 4188

European-Non Finnish (NFE) AF: 0.0000103 AC: 11 AN: 1063638

Other (OTH) AF: 0.00103 AC: 60 AN: 58128

GnomAD4 genome AF: 0.00386 AC: 588 AN: 152236 Hom.: 3 Cov.: 31 AF XY: 0.00366 AC XY: 272 AN XY: 74408

African (AFR) AF: 0.0134 AC: 556 AN: 41542

American (AMR) AF: 0.00118 AC: 18 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.00 AC: 0 AN: 4820

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10596

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 68018

Other (OTH) AF: 0.00523 AC: 11 AN: 2104

Alfa AF: 0.00298 Hom.: 0

Bravo AF: 0.00434

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Nestor-Guillermo progeria syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	6.6
DANN	Benign	0.90
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs145574018; hg19: chr11-65771343;