3-11924917-C-T

Variant names:

• chr3-11924917-C-T
• rs192770

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 0.655 in 152,112 control chromosomes in the GnomAD database, including 32,790 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 0.65 (32790 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.73 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: 0.655 AC: 99518 AN: 151994 Hom.: 32767 Cov.: 33

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.750

Gnomad FIN AF: 0.560

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.655 AC: 99581 AN: 152112 Hom.: 32790 Cov.: 33 AF XY: 0.651 AC XY: 48397 AN XY: 74360

African (AFR) AF: 0.686 AC: 28469 AN: 41480

American (AMR) AF: 0.603 AC: 9216 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.622 AC: 2156 AN: 3468

East Asian (EAS) AF: 0.628 AC: 3244 AN: 5164

South Asian (SAS) AF: 0.751 AC: 3621 AN: 4824

European-Finnish (FIN) AF: 0.560 AC: 5926 AN: 10580

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44850 AN: 67994

Other (OTH) AF: 0.645 AC: 1365 AN: 2116

Alfa AF: 0.645 Hom.: 10303

Bravo AF: 0.652

Asia WGS AF: 0.659 AC: 2292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.0
DANN	Benign	0.70
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs192770; hg19: chr3-11966391;