rs7628864

Variant names:

• chr3-86801468-A-G
• rs7628864

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.296

Gnomad4 EAS AF: 0.632

Gnomad4 SAS AF: 0.386

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.444

Alfa AF: 0.265 Hom.: 637

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7628864; hg19: chr3-86850618;