chr3-194865359-T-C

Variant names:

• chr3-194865359-T-C
• rs11719165

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 0.536 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.323 AC: 13379 AN: 41466

American (AMR) AF: 0.581 AC: 8869 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2215 AN: 3470

East Asian (EAS) AF: 0.455 AC: 2354 AN: 5168

South Asian (SAS) AF: 0.586 AC: 2822 AN: 4812

European-Finnish (FIN) AF: 0.605 AC: 6392 AN: 10566

Middle Eastern (MID) AF: 0.633 AC: 186 AN: 294

European-Non Finnish (NFE) AF: 0.641 AC: 43588 AN: 67984

Other (OTH) AF: 0.576 AC: 1216 AN: 2112

Alfa AF: 0.602 Hom.: 91780

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
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs11719165; hg19: chr3-194586088;