16-171058-T-C

Variant names:

• chr16-171058-T-C
• rs2974771

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 0.55 in 151,622 control chromosomes in the GnomAD database, including 23,268 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 0.55 (23268 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.781
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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: 0.550 AC: 83300 AN: 151504 Hom.: 23239 Cov.: 29

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.501

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.550 AC: 83375 AN: 151622 Hom.: 23268 Cov.: 29 AF XY: 0.545 AC XY: 40371 AN XY: 74048

African (AFR) AF: 0.631 AC: 26098 AN: 41328

American (AMR) AF: 0.500 AC: 7624 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1733 AN: 3462

East Asian (EAS) AF: 0.424 AC: 2169 AN: 5116

South Asian (SAS) AF: 0.439 AC: 2106 AN: 4796

European-Finnish (FIN) AF: 0.516 AC: 5394 AN: 10458

Middle Eastern (MID) AF: 0.514 AC: 150 AN: 292

European-Non Finnish (NFE) AF: 0.538 AC: 36506 AN: 67906

Other (OTH) AF: 0.523 AC: 1099 AN: 2100

Alfa AF: 0.537 Hom.: 33739

Bravo AF: 0.554

Asia WGS AF: 0.453 AC: 1560 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.42
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs2974771; hg19: chr16-221057;