rs6503475

Variant names:

• chr17-43733640-G-A
• rs6503475

Your query was ambiguous. Multiple possible variants found:

• chr17-43733640-G-A
• chr17-43733640-G-T

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 0.583 in 152,052 control chromosomes in the GnomAD database, including 26,696 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 0.58 (26696 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 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: 0.583 AC: 88562 AN: 151934 Hom.: 26673 Cov.: 32

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.640

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.568

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

GnomAD4 genome AF: 0.583 AC: 88606 AN: 152052 Hom.: 26696 Cov.: 32 AF XY: 0.588 AC XY: 43691 AN XY: 74318

African (AFR) AF: 0.447 AC: 18522 AN: 41466

American (AMR) AF: 0.578 AC: 8842 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.640 AC: 2219 AN: 3466

East Asian (EAS) AF: 0.420 AC: 2162 AN: 5150

South Asian (SAS) AF: 0.672 AC: 3231 AN: 4808

European-Finnish (FIN) AF: 0.764 AC: 8096 AN: 10598

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.642 AC: 43605 AN: 67958

Other (OTH) AF: 0.571 AC: 1208 AN: 2114

Alfa AF: 0.610 Hom.: 3571

Bravo AF: 0.559

Asia WGS AF: 0.542 AC: 1884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	5.8
DANN	Benign	0.89
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs6503475; hg19: chr17-41811008;