16-58630161-G-T

Variant names:

• chr16-58630161-G-T
• rs27097

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 0.758 in 152,202 control chromosomes in the GnomAD database, including 44,028 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 0.76 (44028 hom., cov: 35)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.758 AC: 115214 AN: 152084 Hom.: 43992 Cov.: 35

Gnomad AFR AF: 0.843

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.743

Gnomad EAS AF: 0.650

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.721

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.745

Gnomad OTH AF: 0.774

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

GnomAD4 genome AF: 0.758 AC: 115300 AN: 152202 Hom.: 44028 Cov.: 35 AF XY: 0.752 AC XY: 55978 AN XY: 74408

African (AFR) AF: 0.843 AC: 35012 AN: 41546

American (AMR) AF: 0.672 AC: 10264 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.743 AC: 2578 AN: 3468

East Asian (EAS) AF: 0.651 AC: 3364 AN: 5170

South Asian (SAS) AF: 0.668 AC: 3228 AN: 4830

European-Finnish (FIN) AF: 0.721 AC: 7633 AN: 10594

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.745 AC: 50649 AN: 67996

Other (OTH) AF: 0.770 AC: 1628 AN: 2114

Alfa AF: 0.747 Hom.: 51926

Bravo AF: 0.759

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.83
DANN	Benign	0.72
PhyloP100		-1.0
PromoterAI		-0.057	Neutral

Splicing

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

Other links and lift over

dbSNP: rs27097; hg19: chr16-58664065;