rs9525438

Variant names:

• chr13-40964123-A-G
• rs9525438
• NM_172373.4:c.73-5107T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_172373.4(ELF1):​c.73-5107T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.552 in 152,052 control chromosomes in the GnomAD database, including 26,482 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 0.55 (26482 hom., cov: 31)
• Consequence: ELF1 NM_172373.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.30
• Publications: 13 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELF1	NM_172373.4	c.73-5107T>C		intron_variant	Intron 2 of 8	ENST00000239882.7	NP_758961.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ELF1	ENST00000239882.7	c.73-5107T>C		intron_variant	Intron 2 of 8	1	NM_172373.4	ENSP00000239882.3
ELF1	ENST00000635415.1	c.73-5107T>C		intron_variant	Intron 2 of 8	5		ENSP00000489586.1
ELF1	ENST00000625359.1	c.73-5107T>C		intron_variant	Intron 1 of 7	2		ENSP00000486912.1
ELF1	ENST00000498824.5	n.73-5107T>C		intron_variant	Intron 1 of 8	2		ENSP00000487240.1

Frequencies

GnomAD3 genomes AF: 0.553 AC: 84002 AN: 151936 Hom.: 26491 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.786

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.723

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.552 AC: 83994 AN: 152052 Hom.: 26482 Cov.: 31 AF XY: 0.556 AC XY: 41345 AN XY: 74354

African (AFR) AF: 0.258 AC: 10683 AN: 41436

American (AMR) AF: 0.661 AC: 10109 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2224 AN: 3472

East Asian (EAS) AF: 0.180 AC: 935 AN: 5182

South Asian (SAS) AF: 0.574 AC: 2768 AN: 4820

European-Finnish (FIN) AF: 0.723 AC: 7635 AN: 10558

Middle Eastern (MID) AF: 0.651 AC: 190 AN: 292

European-Non Finnish (NFE) AF: 0.699 AC: 47512 AN: 67978

Other (OTH) AF: 0.579 AC: 1221 AN: 2110

Alfa AF: 0.600 Hom.: 5775

Bravo AF: 0.537

Asia WGS AF: 0.341 AC: 1187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.16
DANN	Benign	0.69
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs9525438; hg19: chr13-41538259; COSMIC: COSV53502504;