rs651164

Positions:

• chr6-160160342-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;