rs1923608

Variant names:

• chr6-165207963-G-A
• rs1923608

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 0.217 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.217 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

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.178

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.223

Alfa AF: 0.208 Hom.: 3137

Bravo AF: 0.223

Asia WGS AF: 0.240 AC: 833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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