rs16939136

Variant names:

• chr8-75705060-T-A
• rs16939136

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.13 in 151,830 control chromosomes in the GnomAD database, including 1,361 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 0.13 (1361 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.120

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.192 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: 0.130 AC: 19682 AN: 151712 Hom.: 1363 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.130 AC: 19678 AN: 151830 Hom.: 1361 Cov.: 32 AF XY: 0.128 AC XY: 9530 AN XY: 74216

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.106

Gnomad4 ASJ AF: 0.113

Gnomad4 EAS AF: 0.0153

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0991

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.141

Alfa AF: 0.128 Hom.: 183

Bravo AF: 0.129

Asia WGS AF: 0.133 AC: 460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	18
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16939136; hg19: chr8-76617295;