chr3-176209663-G-A

Variant names:

• chr3-176209663-G-A
• rs11923600

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 0.163 in 152,058 control chromosomes in the GnomAD database, including 2,160 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 0.16 (2160 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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: 0.163 AC: 24792 AN: 151940 Hom.: 2158 Cov.: 33

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.101

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.163 AC: 24828 AN: 152058 Hom.: 2160 Cov.: 33 AF XY: 0.163 AC XY: 12079 AN XY: 74320

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.297

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.116

Gnomad4 NFE AF: 0.142

Gnomad4 OTH AF: 0.152

Alfa AF: 0.143 Hom.: 2502

Bravo AF: 0.169

Asia WGS AF: 0.221 AC: 767 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.52
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11923600; hg19: chr3-175927451;