17-1405534-A-G

Variant names:

• chr17-1405534-A-G
• rs1532976

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 0.738 in 152,074 control chromosomes in the GnomAD database, including 42,793 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 0.74 (42793 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.922 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: 0.738 AC: 112086 AN: 151958 Hom.: 42726 Cov.: 31

Gnomad AFR AF: 0.930

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.667

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.673

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.658

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.738 AC: 112218 AN: 152074 Hom.: 42793 Cov.: 31 AF XY: 0.732 AC XY: 54394 AN XY: 74290

African (AFR) AF: 0.930 AC: 38611 AN: 41532

American (AMR) AF: 0.791 AC: 12057 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 2315 AN: 3472

East Asian (EAS) AF: 0.477 AC: 2461 AN: 5156

South Asian (SAS) AF: 0.672 AC: 3238 AN: 4820

European-Finnish (FIN) AF: 0.618 AC: 6528 AN: 10560

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.658 AC: 44711 AN: 67982

Other (OTH) AF: 0.733 AC: 1544 AN: 2106

Alfa AF: 0.682 Hom.: 53333

Bravo AF: 0.757

Asia WGS AF: 0.626 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.47
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1532976; hg19: chr17-1308828;