3-161786219-C-T

Variant names:

• chr3-161786219-C-T
• rs1996264

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.444 in 151,720 control chromosomes in the GnomAD database, including 15,648 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 0.44 (15648 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.29

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.824 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: 0.444 AC: 67343 AN: 151604 Hom.: 15630 Cov.: 31

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.447

Gnomad EAS AF: 0.845

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.444 AC: 67388 AN: 151720 Hom.: 15648 Cov.: 31 AF XY: 0.450 AC XY: 33401 AN XY: 74150

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.496

Gnomad4 ASJ AF: 0.447

Gnomad4 EAS AF: 0.845

Gnomad4 SAS AF: 0.408

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.434

Alfa AF: 0.447 Hom.: 27152

Bravo AF: 0.447

Asia WGS AF: 0.633 AC: 2197 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	17
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1996264; hg19: chr3-161504007;