Variant 13-40941085-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_172373.4(ELF1):c.1092A>T(p.Pro364=) 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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.0980

Variant links:

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]

ELF1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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 id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELF1	NM_172373.4 linkuse as main transcript	c.1092A>T	p.Pro364=	synonymous_variant	8/9	ENST00000239882.7	NP_758961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELF1	ENST00000239882.7 linkuse as main transcript	c.1092A>T	p.Pro364=	synonymous_variant	8/9	1	NM_172373.4	ENSP00000239882	P1	P32519-1
ELF1	ENST00000635415.1 linkuse as main transcript	c.1092A>T	p.Pro364=	synonymous_variant	8/9	5		ENSP00000489586
ELF1	ENST00000625359.1 linkuse as main transcript	c.1020A>T	p.Pro340=	synonymous_variant	7/8	2		ENSP00000486912		P32519-2
ELF1	ENST00000498824.4 linkuse as main transcript	c.*835A>T		3_prime_UTR_variant, NMD_transcript_variant	8/9	2		ENSP00000487240

Frequencies

GnomAD3 genomes

AF:

0.00574

AC:

873

AN:

152194

Hom.:

Cov.:

show subpopulations

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

GnomAD3 exomes

AF:

0.00722

AC:

1816

AN:

251490

Hom.:

AF XY:

0.00779

AC XY:

1059

AN XY:

135918

show subpopulations

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 SAS exome

AF:

0.0142

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.:

Cov.:

AF XY:

0.00878

AC XY:

6386

AN XY:

727244

show subpopulations

Gnomad4 AFR exome

AF:

0.00167

Gnomad4 AMR exome

AF:

0.00313

Gnomad4 ASJ exome

AF:

0.0126

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.0144

Gnomad4 FIN exome

AF:

0.00760

Gnomad4 NFE exome

AF:

0.00892

Gnomad4 OTH exome

AF:

0.00666

GnomAD4 genome

AF:

0.00573

AC:

873

AN:

152312

Hom.:

Cov.:

AF XY:

0.00577

AC XY:

430

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.00166

Gnomad4 AMR

AF:

0.00327

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0143

Gnomad4 FIN

AF:

0.00829

Gnomad4 NFE

AF:

0.00791

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.00775

Hom.:

Bravo

AF:

0.00491

Asia WGS

AF:

0.00520

AC:

AN:

3478

EpiCase

AF:

0.00682

EpiControl

AF:

0.00842

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 12, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.31

DANN

Benign

0.40

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over