rs8073390

Positions:

• chr17-57042633-C-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.0956 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

Gnomad4 AFR AF: 0.0307

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0674

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.137

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.0749

Alfa AF: 0.143 Hom.: 46

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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