rs651164

Variant names:

• chr6-160160342-A-G
• rs651164

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 0.684 in 152,126 control chromosomes in the GnomAD database, including 35,974 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 0.68 (35974 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.741 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: 0.684 AC: 104022 AN: 152008 Hom.: 35935 Cov.: 33

Gnomad AFR AF: 0.748

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.635

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.428

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.684 AC: 104114 AN: 152126 Hom.: 35974 Cov.: 33 AF XY: 0.678 AC XY: 50445 AN XY: 74376

Gnomad4 AFR AF: 0.748

Gnomad4 AMR AF: 0.635

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.574

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.674

Alfa AF: 0.684 Hom.: 40263

Bravo AF: 0.686

Asia WGS AF: 0.531 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs651164; hg19: chr6-160581374; COSMIC: COSV61451926;