rs7647854

Variant names:

• chr3-185158995-G-A
• rs7647854

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 0.796 in 152,024 control chromosomes in the GnomAD database, including 48,322 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 0.80 (48322 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.425

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.831 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: 0.796 AC: 120920 AN: 151906 Hom.: 48273 Cov.: 31

Gnomad AFR AF: 0.725

Gnomad AMI AF: 0.794

Gnomad AMR AF: 0.819

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.793

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.803

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.814

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

GnomAD4 genome AF: 0.796 AC: 121031 AN: 152024 Hom.: 48322 Cov.: 31 AF XY: 0.793 AC XY: 58875 AN XY: 74282

Gnomad4 AFR AF: 0.726

Gnomad4 AMR AF: 0.819

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.793

Gnomad4 SAS AF: 0.788

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.815

Alfa AF: 0.833 Hom.: 114307

Bravo AF: 0.796

Asia WGS AF: 0.808 AC: 2810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7647854; hg19: chr3-184876783;