17-42394249-T-C

Variant names:

• chr17-42394249-T-C
• rs16967738

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 0.0928 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
• Publications: 6 publications found

ACMG classification

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

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

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.137 AC: 5696 AN: 41516

American (AMR) AF: 0.0594 AC: 907 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 157 AN: 3472

East Asian (EAS) AF: 0.0177 AC: 92 AN: 5190

South Asian (SAS) AF: 0.0735 AC: 355 AN: 4830

European-Finnish (FIN) AF: 0.121 AC: 1282 AN: 10586

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0784 AC: 5332 AN: 68008

Other (OTH) AF: 0.0757 AC: 160 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.40
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs16967738; hg19: chr17-40546267;