rs16938754

Variant names:

• chr8-73990814-T-G
• rs16938754

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0156 in 152,272 control chromosomes in the GnomAD database, including 29 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 0.016 (29 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.0156 (2369/152272) while in subpopulation SAS AF = 0.0216 (104/4824). AF 95% confidence interval is 0.0182. There are 29 homozygotes in GnomAd4. There are 1287 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 29 gene

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: 0.0156 AC: 2367 AN: 152154 Hom.: 29 Cov.: 32

Gnomad AFR AF: 0.00311

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0120

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.0152

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0153

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

GnomAD4 genome AF: 0.0156 AC: 2369 AN: 152272 Hom.: 29 Cov.: 32 AF XY: 0.0173 AC XY: 1287 AN XY: 74458

African (AFR) AF: 0.00310 AC: 129 AN: 41554

American (AMR) AF: 0.0120 AC: 184 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0190 AC: 66 AN: 3470

East Asian (EAS) AF: 0.0152 AC: 79 AN: 5182

South Asian (SAS) AF: 0.0216 AC: 104 AN: 4824

European-Finnish (FIN) AF: 0.0472 AC: 501 AN: 10612

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0186 AC: 1264 AN: 68018

Other (OTH) AF: 0.0161 AC: 34 AN: 2110

Alfa AF: 0.0161 Hom.: 45

Bravo AF: 0.0123

Asia WGS AF: 0.0230 AC: 78 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	8.2
DANN	Benign	0.85
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs16938754; hg19: chr8-74903049;