rs1965861

chr6-159461689-A-Gchr6-159461689-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 0.627 in 151,976 control chromosomes in the GnomAD database, including 30,370 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 0.63 (30370 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.154

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 (SAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95241 AN: 151858 Hom.: 30323 Cov.: 32

Gnomad AFR AF: 0.511

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.728

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.627 AC: 95346 AN: 151976 Hom.: 30370 Cov.: 32 AF XY: 0.632 AC XY: 46931 AN XY: 74278

Gnomad4 AFR AF: 0.512

Gnomad4 AMR AF: 0.665

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.658

Gnomad4 OTH AF: 0.634

Alfa AF: 0.620 Hom.: 3636

Bravo AF: 0.617

Asia WGS AF: 0.703 AC: 2440 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	4.0
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1965861; hg19: chr6-159882721;