16-27307444-G-T

Variant names:

• chr16-27307444-G-T
• rs4787947

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 0.917 in 151,546 control chromosomes in the GnomAD database, including 63,811 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 0.92 (63811 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.176
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 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: 0.917 AC: 138794 AN: 151430 Hom.: 63762 Cov.: 28

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.909

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.884

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.908

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.917 AC: 138894 AN: 151546 Hom.: 63811 Cov.: 28 AF XY: 0.915 AC XY: 67767 AN XY: 74038

African (AFR) AF: 0.969 AC: 39875 AN: 41164

American (AMR) AF: 0.833 AC: 12647 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3012 AN: 3468

East Asian (EAS) AF: 0.914 AC: 4721 AN: 5168

South Asian (SAS) AF: 0.883 AC: 4239 AN: 4802

European-Finnish (FIN) AF: 0.924 AC: 9671 AN: 10468

Middle Eastern (MID) AF: 0.866 AC: 253 AN: 292

European-Non Finnish (NFE) AF: 0.908 AC: 61727 AN: 67988

Other (OTH) AF: 0.912 AC: 1920 AN: 2106

Alfa AF: 0.907 Hom.: 103773

Bravo AF: 0.914

Asia WGS AF: 0.888 AC: 3088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.55
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs4787947; hg19: chr16-27318765;