rs9532691

chr13-40969358-T-C

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• 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/exons	MANE	UniProt
ELF1	NM_172373.4	c.73-10342A>G		intron_variant		ENST00000239882.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ELF1	ENST00000239882.7	c.73-10342A>G		intron_variant		1	NM_172373.4	P1
ELF1	ENST00000625359.1	c.73-10342A>G		intron_variant		2
ELF1	ENST00000635415.1	c.73-10342A>G		intron_variant		5
ELF1	ENST00000498824.4	c.73-10342A>G		intron_variant, NMD_transcript_variant		2

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

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.639

Gnomad4 EAS AF: 0.182

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.574

Alfa AF: 0.607 Hom.: 5022

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

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: rs9532691; hg19: chr13-41543494;