rs16906958

Variant names:

• chr8-79608410-G-A
• rs16906958

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 0.061 in 152,200 control chromosomes in the GnomAD database, including 494 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 0.061 (494 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.203 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: 0.0608 AC: 9248 AN: 152082 Hom.: 488 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.00980

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.0176

Gnomad FIN AF: 0.0146

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0201

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0610 AC: 9286 AN: 152200 Hom.: 494 Cov.: 33 AF XY: 0.0609 AC XY: 4535 AN XY: 74426

African (AFR) AF: 0.124 AC: 5130 AN: 41516

American (AMR) AF: 0.0749 AC: 1145 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00980 AC: 34 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1105 AN: 5184

South Asian (SAS) AF: 0.0176 AC: 85 AN: 4816

European-Finnish (FIN) AF: 0.0146 AC: 155 AN: 10610

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.0201 AC: 1367 AN: 68000

Other (OTH) AF: 0.0442 AC: 93 AN: 2106

Alfa AF: 0.0339 Hom.: 935

Bravo AF: 0.0704

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.56
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs16906958; hg19: chr8-80520645;