17-34501507-A-T

Variant names:

• chr17-34501507-A-T
• rs190038

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 0.0559 in 152,218 control chromosomes in the GnomAD database, including 719 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 0.056 (719 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 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: 0.0560 AC: 8516 AN: 152100 Hom.: 720 Cov.: 32

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0924

Gnomad ASJ AF: 0.0207

Gnomad EAS AF: 0.407

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.0854

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0142

Gnomad OTH AF: 0.0431

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

GnomAD4 genome AF: 0.0559 AC: 8508 AN: 152218 Hom.: 719 Cov.: 32 AF XY: 0.0637 AC XY: 4743 AN XY: 74416

African (AFR) AF: 0.0523 AC: 2172 AN: 41550

American (AMR) AF: 0.0923 AC: 1412 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0207 AC: 72 AN: 3470

East Asian (EAS) AF: 0.407 AC: 2098 AN: 5154

South Asian (SAS) AF: 0.165 AC: 795 AN: 4816

European-Finnish (FIN) AF: 0.0854 AC: 905 AN: 10602

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0142 AC: 963 AN: 68018

Other (OTH) AF: 0.0422 AC: 89 AN: 2110

Alfa AF: 0.0329 Hom.: 20

Bravo AF: 0.0598

Asia WGS AF: 0.261 AC: 906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.45
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs190038; hg19: chr17-32828526;