chr13-40941085-T-A

Variant names:

• chr13-40941085-T-A
• rs151034333
• NM_172373.4:c.1092A>T

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_Strong BP6_Very_Strong BP7 BS2

The NM_172373.4(ELF1):​c.1092A>T​(p.Pro364Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0083 in 1,614,202 control chromosomes in the GnomAD database, including 93 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0057 (8 hom., cov: 32)
  • Exomes 𝑓: 0.0086 (85 hom.)
• Consequence: ELF1 NM_172373.4 synonymous
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.0980
• Publications: 2 publications found

Genes affected

ELF1 (HGNC:3316): (E74 like ETS transcription factor 1) This gene encodes an E26 transformation-specific related transcription factor. The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2009]

ACMG classification

Our verdict: Benign. The variant received -17 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 13-40941085-T-A is Benign according to our data. Variant chr13-40941085-T-A is described in ClinVar as Benign. ClinVar VariationId is 771190.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BP7: Synonymous conserved (PhyloP=-0.098 with no splicing effect.
• BS2: High AC in GnomAd4 at 873 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172373.4. 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
	ELF1	NM_172373.4	MANE Select	c.1092A>T	p.Pro364Pro	synonymous	Exon 8 of 9	NP_758961.1	P32519-1
	ELF1	NM_001370330.1		c.1092A>T	p.Pro364Pro	synonymous	Exon 8 of 9	NP_001357259.1	P32519-1
	ELF1	NM_001370331.1		c.1092A>T	p.Pro364Pro	synonymous	Exon 8 of 9	NP_001357260.1	P32519-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ELF1	ENST00000239882.7	TSL:1 MANE Select	c.1092A>T	p.Pro364Pro	synonymous	Exon 8 of 9	ENSP00000239882.3	P32519-1
	ELF1	ENST00000891312.1		c.1092A>T	p.Pro364Pro	synonymous	Exon 9 of 10	ENSP00000561371.1
	ELF1	ENST00000891313.1		c.1092A>T	p.Pro364Pro	synonymous	Exon 9 of 10	ENSP00000561372.1

Frequencies

GnomAD3 genomes AF: 0.00574 AC: 873 AN: 152194 Hom.: 8 Cov.: 32

Gnomad AFR AF: 0.00166

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.00327

Gnomad ASJ AF: 0.0107

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.00829

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00791

Gnomad OTH AF: 0.00478

GnomAD2 exomes AF: 0.00722 AC: 1816 AN: 251490 AF XY: 0.00779

Gnomad AFR exome AF: 0.00154

Gnomad AMR exome AF: 0.00283

Gnomad ASJ exome AF: 0.0114

Gnomad EAS exome AF: 0.0000544

Gnomad FIN exome AF: 0.00864

Gnomad NFE exome AF: 0.00809

Gnomad OTH exome AF: 0.00586

GnomAD4 exome AF: 0.00856 AC: 12520 AN: 1461890 Hom.: 85 Cov.: 29 AF XY: 0.00878 AC XY: 6386 AN XY: 727244

African (AFR) AF: 0.00167 AC: 56 AN: 33480

American (AMR) AF: 0.00313 AC: 140 AN: 44724

Ashkenazi Jewish (ASJ) AF: 0.0126 AC: 330 AN: 26136

East Asian (EAS) AF: 0.0000252 AC: 1 AN: 39698

South Asian (SAS) AF: 0.0144 AC: 1243 AN: 86258

European-Finnish (FIN) AF: 0.00760 AC: 406 AN: 53418

Middle Eastern (MID) AF: 0.00312 AC: 18 AN: 5768

European-Non Finnish (NFE) AF: 0.00892 AC: 9924 AN: 1112012

Other (OTH) AF: 0.00666 AC: 402 AN: 60396

GnomAD4 genome AF: 0.00573 AC: 873 AN: 152312 Hom.: 8 Cov.: 32 AF XY: 0.00577 AC XY: 430 AN XY: 74488

African (AFR) AF: 0.00166 AC: 69 AN: 41578

American (AMR) AF: 0.00327 AC: 50 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0107 AC: 37 AN: 3468

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5182

South Asian (SAS) AF: 0.0143 AC: 69 AN: 4822

European-Finnish (FIN) AF: 0.00829 AC: 88 AN: 10618

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.00791 AC: 538 AN: 68026

Other (OTH) AF: 0.00473 AC: 10 AN: 2114

Alfa AF: 0.00775 Hom.: 2

Bravo AF: 0.00491

Asia WGS AF: 0.00520 AC: 18 AN: 3478

EpiCase AF: 0.00682

EpiControl AF: 0.00842

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.31
DANN	Benign	0.40
PhyloP100		-0.098
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: rs151034333; hg19: chr13-41515221;