rs6752979

Variant names:

• chr2-81514626-G-A
• rs6752979
• ENST00000817540.1:n.372+32522G>A

Your query was ambiguous. Multiple possible variants found:

• chr2-81514626-G-A
• chr2-81514626-G-T

Variant summary

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

The ENST00000817540.1(ENSG00000306384):​n.372+32522G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,934 control chromosomes in the GnomAD database, including 12,394 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 0.37 (12394 hom., cov: 32)
• Consequence: ENSG00000306384 ENST00000817540.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 6 publications found

Genes affected

ENSG00000306384 (HGNC:):

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 (AFR) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000817540.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC102724542	NR_187691.1		n.367+32522G>A		intron	N/A
	LOC102724542	NR_187692.1		n.367+32522G>A		intron	N/A
	LOC102724542	NR_187693.1		n.367+32522G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306384	ENST00000817540.1		n.372+32522G>A		intron	N/A
	ENSG00000306384	ENST00000817541.1		n.370+32522G>A		intron	N/A
	ENSG00000306384	ENST00000817542.1		n.365+32522G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56818 AN: 151816 Hom.: 12347 Cov.: 32

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.149

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.375 AC: 56915 AN: 151934 Hom.: 12394 Cov.: 32 AF XY: 0.365 AC XY: 27069 AN XY: 74252

African (AFR) AF: 0.608 AC: 25191 AN: 41406

American (AMR) AF: 0.238 AC: 3636 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1005 AN: 3464

East Asian (EAS) AF: 0.149 AC: 765 AN: 5150

South Asian (SAS) AF: 0.118 AC: 569 AN: 4808

European-Finnish (FIN) AF: 0.304 AC: 3213 AN: 10556

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21412 AN: 67962

Other (OTH) AF: 0.306 AC: 643 AN: 2104

Alfa AF: 0.316 Hom.: 13060

Bravo AF: 0.381

Asia WGS AF: 0.170 AC: 591 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	4.1
DANN	Benign	0.68
PhyloP100		0.080

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6752979; hg19: chr2-81741750;