17-57042633-C-T

Variant names:

• chr17-57042633-C-T
• rs8073390

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.095 (175 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.34
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 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: 0.0956 AC: 5333 AN: 55774 Hom.: 175 Cov.: 0

Gnomad AFR AF: 0.0308

Gnomad AMI AF: 0.0186

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0674

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.137

Gnomad MID AF: 0.148

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0765

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

GnomAD4 genome AF: 0.0954 AC: 5327 AN: 55826 Hom.: 175 Cov.: 0 AF XY: 0.0932 AC XY: 2480 AN XY: 26604

African (AFR) AF: 0.0307 AC: 364 AN: 11868

American (AMR) AF: 0.103 AC: 480 AN: 4664

Ashkenazi Jewish (ASJ) AF: 0.0674 AC: 104 AN: 1542

East Asian (EAS) AF: 0.172 AC: 219 AN: 1270

South Asian (SAS) AF: 0.160 AC: 257 AN: 1610

European-Finnish (FIN) AF: 0.137 AC: 420 AN: 3066

Middle Eastern (MID) AF: 0.130 AC: 13 AN: 100

European-Non Finnish (NFE) AF: 0.112 AC: 3409 AN: 30568

Other (OTH) AF: 0.0749 AC: 53 AN: 708

Alfa AF: 0.143 Hom.: 46

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.30
DANN	Benign	0.090
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs8073390; hg19: chr17-55119994; COSMIC: COSV73849959;