17-42390192-G-C

Variant names:

• chr17-42390192-G-C
• rs4796793

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 0.674 in 151,998 control chromosomes in the GnomAD database, including 35,647 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 0.67 (35647 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 82 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.786 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: 0.674 AC: 102427 AN: 151880 Hom.: 35614 Cov.: 32

Gnomad AFR AF: 0.504

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.604

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.674 AC: 102521 AN: 151998 Hom.: 35647 Cov.: 32 AF XY: 0.674 AC XY: 50101 AN XY: 74280

African (AFR) AF: 0.505 AC: 20906 AN: 41408

American (AMR) AF: 0.798 AC: 12182 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.692 AC: 2400 AN: 3470

East Asian (EAS) AF: 0.604 AC: 3129 AN: 5184

South Asian (SAS) AF: 0.639 AC: 3078 AN: 4818

European-Finnish (FIN) AF: 0.734 AC: 7742 AN: 10548

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.746 AC: 50706 AN: 67990

Other (OTH) AF: 0.697 AC: 1471 AN: 2110

Alfa AF: 0.648 Hom.: 2233

Bravo AF: 0.670

Asia WGS AF: 0.600 AC: 2091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.46
DANN	Benign	0.55
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs4796793; hg19: chr17-40542210;