17-57031373-A-T

Variant names:

• chr17-57031373-A-T
• rs6503782

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 0.554 in 151,926 control chromosomes in the GnomAD database, including 24,221 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 0.55 (24221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.298
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.773 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: 0.554 AC: 84096 AN: 151808 Hom.: 24174 Cov.: 32

Gnomad AFR AF: 0.696

Gnomad AMI AF: 0.454

Gnomad AMR AF: 0.488

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.794

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.554 AC: 84200 AN: 151926 Hom.: 24221 Cov.: 32 AF XY: 0.554 AC XY: 41172 AN XY: 74274

African (AFR) AF: 0.697 AC: 28887 AN: 41452

American (AMR) AF: 0.488 AC: 7427 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.551 AC: 1913 AN: 3470

East Asian (EAS) AF: 0.793 AC: 4108 AN: 5180

South Asian (SAS) AF: 0.628 AC: 3019 AN: 4810

European-Finnish (FIN) AF: 0.479 AC: 5046 AN: 10544

Middle Eastern (MID) AF: 0.582 AC: 170 AN: 292

European-Non Finnish (NFE) AF: 0.471 AC: 32036 AN: 67950

Other (OTH) AF: 0.560 AC: 1181 AN: 2110

Alfa AF: 0.511 Hom.: 2534

Bravo AF: 0.559

Asia WGS AF: 0.737 AC: 2563 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.80
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6503782; hg19: chr17-55108734;