rs7644516

Variant names:

• chr3-25880794-G-A
• rs7644516
• ENST00000829679.1:n.276+6791G>A

Variant summary

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

The ENST00000829679.1(ENSG00000307904):​n.276+6791G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.926 in 152,306 control chromosomes in the GnomAD database, including 65,413 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 0.93 (65413 hom., cov: 33)
• Consequence: ENSG00000307904 ENST00000829679.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412
• Publications: 4 publications found

Genes affected

ENSG00000307904 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000829679.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000307904	ENST00000829679.1		n.276+6791G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.926 AC: 140881 AN: 152188 Hom.: 65350 Cov.: 33

Gnomad AFR AF: 0.978

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.908

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.881

Gnomad FIN AF: 0.941

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.926 AC: 141006 AN: 152306 Hom.: 65413 Cov.: 33 AF XY: 0.928 AC XY: 69086 AN XY: 74462

African (AFR) AF: 0.978 AC: 40680 AN: 41580

American (AMR) AF: 0.920 AC: 14072 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.908 AC: 3153 AN: 3472

East Asian (EAS) AF: 0.987 AC: 5125 AN: 5190

South Asian (SAS) AF: 0.881 AC: 4250 AN: 4824

European-Finnish (FIN) AF: 0.941 AC: 9987 AN: 10614

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60700 AN: 68012

Other (OTH) AF: 0.926 AC: 1960 AN: 2116

Alfa AF: 0.901 Hom.: 34992

Bravo AF: 0.926

Asia WGS AF: 0.922 AC: 3201 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.3
DANN	Benign	0.42
PhyloP100		0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7644516;

hg19: chr3-25922285;