rs1923608

Variant names:

• chr6-165207963-G-A
• rs1923608

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.217 in 152,070 control chromosomes in the GnomAD database, including 3,809 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 0.22 (3809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32983 AN: 151952 Hom.: 3797 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.217 AC: 33034 AN: 152070 Hom.: 3809 Cov.: 32 AF XY: 0.222 AC XY: 16538 AN XY: 74332

African (AFR) AF: 0.187 AC: 7747 AN: 41480

American (AMR) AF: 0.318 AC: 4854 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3472

East Asian (EAS) AF: 0.319 AC: 1642 AN: 5152

South Asian (SAS) AF: 0.178 AC: 858 AN: 4822

European-Finnish (FIN) AF: 0.281 AC: 2974 AN: 10566

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13718 AN: 67984

Other (OTH) AF: 0.223 AC: 471 AN: 2110

Alfa AF: 0.209 Hom.: 4641

Bravo AF: 0.223

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.6
DANN	Benign	0.47
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1923608; hg19: chr6-165621452; COSMIC: COSV60302115;