chr3-194865359-T-C

Variant names:

• chr3-194865359-T-C
• rs11719165

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 0.536 in 152,048 control chromosomes in the GnomAD database, including 23,427 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 0.54 (23427 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.559

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.636 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: 0.536 AC: 81469 AN: 151930 Hom.: 23420 Cov.: 33

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.522

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.457

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.641

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.536 AC: 81496 AN: 152048 Hom.: 23427 Cov.: 33 AF XY: 0.536 AC XY: 39818 AN XY: 74320

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.638

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.641

Gnomad4 OTH AF: 0.576

Alfa AF: 0.620 Hom.: 40904

Bravo AF: 0.527

Asia WGS AF: 0.498 AC: 1730 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	9.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11719165; hg19: chr3-194586088;