rs16967738

Positions:

• chr17-42394249-T-C

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 0.0928 in 152,204 control chromosomes in the GnomAD database, including 772 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 0.093 (772 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.571

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0926 AC: 14085 AN: 152086 Hom.: 764 Cov.: 32

Gnomad AFR AF: 0.137

Gnomad AMI AF: 0.137

Gnomad AMR AF: 0.0594

Gnomad ASJ AF: 0.0452

Gnomad EAS AF: 0.0177

Gnomad SAS AF: 0.0734

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0784

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0928 AC: 14124 AN: 152204 Hom.: 772 Cov.: 32 AF XY: 0.0930 AC XY: 6926 AN XY: 74434

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0594

Gnomad4 ASJ AF: 0.0452

Gnomad4 EAS AF: 0.0177

Gnomad4 SAS AF: 0.0735

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0784

Gnomad4 OTH AF: 0.0757

Alfa AF: 0.0943 Hom.: 93

Bravo AF: 0.0876

Asia WGS AF: 0.0930 AC: 324 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	4.9
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16967738; hg19: chr17-40546267;