3-196107486-G-C

Variant names:

• chr3-196107486-G-C
• rs11717368

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 0.606 in 151,978 control chromosomes in the GnomAD database, including 29,052 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 0.61 (29052 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91989 AN: 151862 Hom.: 29017 Cov.: 31

Gnomad AFR AF: 0.792

Gnomad AMI AF: 0.455

Gnomad AMR AF: 0.617

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.496

Gnomad FIN AF: 0.498

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.601

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

GnomAD4 genome AF: 0.606 AC: 92086 AN: 151978 Hom.: 29052 Cov.: 31 AF XY: 0.603 AC XY: 44820 AN XY: 74270

African (AFR) AF: 0.792 AC: 32842 AN: 41466

American (AMR) AF: 0.616 AC: 9394 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3663 AN: 5174

South Asian (SAS) AF: 0.497 AC: 2394 AN: 4814

European-Finnish (FIN) AF: 0.498 AC: 5247 AN: 10544

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35069 AN: 67964

Other (OTH) AF: 0.604 AC: 1266 AN: 2096

Alfa AF: 0.377 Hom.: 859

Bravo AF: 0.627

Asia WGS AF: 0.625 AC: 2175 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
DANN	Benign	0.17
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs11717368; hg19: chr3-195834357;