3-16150636-T-C

Variant names:

• chr3-16150636-T-C
• rs6771632

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 0.501 in 152,038 control chromosomes in the GnomAD database, including 19,461 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 0.50 (19461 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.66 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: 0.501 AC: 76066 AN: 151922 Hom.: 19456 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.679

Gnomad FIN AF: 0.393

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.501 AC: 76109 AN: 152038 Hom.: 19461 Cov.: 32 AF XY: 0.501 AC XY: 37203 AN XY: 74304

African (AFR) AF: 0.445 AC: 18443 AN: 41444

American (AMR) AF: 0.584 AC: 8925 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2325 AN: 3466

East Asian (EAS) AF: 0.535 AC: 2760 AN: 5162

South Asian (SAS) AF: 0.679 AC: 3271 AN: 4814

European-Finnish (FIN) AF: 0.393 AC: 4155 AN: 10566

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.505 AC: 34298 AN: 67984

Other (OTH) AF: 0.564 AC: 1192 AN: 2114

Alfa AF: 0.521 Hom.: 49510

Bravo AF: 0.510

Asia WGS AF: 0.589 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.39
DANN	Benign	0.52
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6771632; hg19: chr3-16192143;