chr16-171127-C-T

Variant names:

• chr16-171127-C-T
• rs57397665

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 0.508 in 151,698 control chromosomes in the GnomAD database, including 19,831 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 0.51 (19831 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.532 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: 0.508 AC: 77022 AN: 151580 Hom.: 19815 Cov.: 31

Gnomad AFR AF: 0.503

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.339

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.493

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

GnomAD4 genome AF: 0.508 AC: 77079 AN: 151698 Hom.: 19831 Cov.: 31 AF XY: 0.504 AC XY: 37336 AN XY: 74076

African (AFR) AF: 0.502 AC: 20779 AN: 41356

American (AMR) AF: 0.476 AC: 7270 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1728 AN: 3466

East Asian (EAS) AF: 0.339 AC: 1747 AN: 5156

South Asian (SAS) AF: 0.434 AC: 2085 AN: 4802

European-Finnish (FIN) AF: 0.512 AC: 5323 AN: 10388

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36458 AN: 67944

Other (OTH) AF: 0.495 AC: 1046 AN: 2112

Alfa AF: 0.483 Hom.: 3985

Bravo AF: 0.516

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.8
DANN	Benign	0.21
PhyloP100		-0.024

Splicing

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

Other links and lift over

dbSNP: rs57397665; hg19: chr16-221126;