rs16938754

Positions:

• chr8-73990814-T-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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 male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 29 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00310

Gnomad4 AMR AF: 0.0120

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.0152

Gnomad4 SAS AF: 0.0216

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.0186

Gnomad4 OTH AF: 0.0161

Alfa AF: 0.0180 Hom.: 36

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16938754; hg19: chr8-74903049;