13-40983974-A-G

Position:

• chr13-40983974-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_172373.4(ELF1):​c.-228-1692T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0477 in 152,242 control chromosomes in the GnomAD database, including 427 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.048 (427 hom., cov: 32)
• Consequence: ELF1 NM_172373.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ELF1	NM_172373.4	c.-228-1692T>C		intron_variant		ENST00000239882.7	NP_758961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ELF1	ENST00000239882.7	c.-228-1692T>C		intron_variant		1	NM_172373.4	ENSP00000239882	P1
ELF1	ENST00000405737.2	c.-228-1692T>C		intron_variant		2		ENSP00000384135

Frequencies

GnomAD3 genomes AF: 0.0475 AC: 7220 AN: 152124 Hom.: 411 Cov.: 32

Gnomad AFR AF: 0.0737

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0812

Gnomad ASJ AF: 0.00432

Gnomad EAS AF: 0.231

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.0771

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00463

Gnomad OTH AF: 0.0435

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0477 AC: 7268 AN: 152242 Hom.: 427 Cov.: 32 AF XY: 0.0524 AC XY: 3904 AN XY: 74436

Gnomad4 AFR AF: 0.0737

Gnomad4 AMR AF: 0.0825

Gnomad4 ASJ AF: 0.00432

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.0771

Gnomad4 NFE AF: 0.00463

Gnomad4 OTH AF: 0.0525

Alfa AF: 0.0192 Hom.: 354

Bravo AF: 0.0479

Asia WGS AF: 0.213 AC: 737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
DANN	Benign	0.70

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

Other links and lift over

dbSNP: rs7329174; hg19: chr13-41558110;