3-196107486-G-C

Variant names:

• chr3-196107486-G-C
• rs11717368

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 0.606 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.606 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

Gnomad4 AFR AF: 0.792

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.497

Gnomad4 FIN AF: 0.498

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.604

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.57
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: rs11717368; hg19: chr3-195834357;