rs9532691

Variant names:

• chr13-40969358-T-C
• rs9532691
• NM_172373.4:c.73-10342A>G

Variant summary

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

The NM_172373.4(ELF1):​c.73-10342A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.547 in 152,096 control chromosomes in the GnomAD database, including 25,890 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 (25890 hom., cov: 31)
• Consequence: ELF1 NM_172373.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 11 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ELF1	NM_172373.4	c.73-10342A>G		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.73-10342A>G		intron_variant	Intron 2 of 8	1	NM_172373.4	ENSP00000239882.3
ELF1	ENST00000635415.1	c.73-10342A>G		intron_variant	Intron 2 of 8	5		ENSP00000489586.1
ELF1	ENST00000625359.1	c.73-10342A>G		intron_variant	Intron 1 of 7	2		ENSP00000486912.1
ELF1	ENST00000498824.5	n.73-10342A>G		intron_variant	Intron 1 of 8	2		ENSP00000487240.1

Frequencies

GnomAD3 genomes AF: 0.548 AC: 83278 AN: 151978 Hom.: 25898 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.785

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.182

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.582

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

GnomAD4 genome AF: 0.547 AC: 83272 AN: 152096 Hom.: 25890 Cov.: 31 AF XY: 0.552 AC XY: 41020 AN XY: 74358

African (AFR) AF: 0.265 AC: 10978 AN: 41498

American (AMR) AF: 0.655 AC: 10005 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2218 AN: 3470

East Asian (EAS) AF: 0.182 AC: 940 AN: 5162

South Asian (SAS) AF: 0.569 AC: 2744 AN: 4824

European-Finnish (FIN) AF: 0.716 AC: 7565 AN: 10560

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46703 AN: 67982

Other (OTH) AF: 0.574 AC: 1214 AN: 2116

Alfa AF: 0.598 Hom.: 5054

Bravo AF: 0.534

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.54
DANN	Benign	0.61
PhyloP100		-0.76
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: rs9532691; hg19: chr13-41543494;