rs7628864

Variant names:

• chr3-86801468-A-G
• rs7628864
• ENST00000760372.1:n.336+1876A>G

Your query was ambiguous. Multiple possible variants found:

• chr3-86801468-A-G
• chr3-86801468-A-T

Variant summary

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

The ENST00000760372.1(ENSG00000299083):​n.336+1876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 145,986 control chromosomes in the GnomAD database, including 14,814 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 0.44 (14814 hom., cov: 28)
• Consequence: ENSG00000299083 ENST00000760372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 11 publications found

Genes affected

ENSG00000299083 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.614 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299083	ENST00000760372.1	n.336+1876A>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.437 AC: 63781 AN: 145980 Hom.: 14803 Cov.: 28

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.510

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.328

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.437 AC: 63789 AN: 145986 Hom.: 14814 Cov.: 28 AF XY: 0.437 AC XY: 31010 AN XY: 70982

African (AFR) AF: 0.531 AC: 21038 AN: 39590

American (AMR) AF: 0.510 AC: 7394 AN: 14506

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1023 AN: 3456

East Asian (EAS) AF: 0.632 AC: 3209 AN: 5078

South Asian (SAS) AF: 0.386 AC: 1824 AN: 4724

European-Finnish (FIN) AF: 0.345 AC: 2935 AN: 8500

Middle Eastern (MID) AF: 0.317 AC: 88 AN: 278

European-Non Finnish (NFE) AF: 0.375 AC: 25080 AN: 66946

Other (OTH) AF: 0.444 AC: 887 AN: 1998

Alfa AF: 0.396 Hom.: 3237

Bravo AF: 0.457

Asia WGS AF: 0.528 AC: 1779 AN: 3374

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.45
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7628864; hg19: chr3-86850618;