rs17203612

Positions:

• chr6-32479076-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.432 in 134,548 control chromosomes in the GnomAD database, including 11,619 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 0.43 (11619 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

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 (AMR) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.432 AC: 58126 AN: 134442 Hom.: 11612 Cov.: 31

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.661

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.483

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.432 AC: 58164 AN: 134548 Hom.: 11619 Cov.: 31 AF XY: 0.431 AC XY: 28409 AN XY: 65912

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.535

Gnomad4 EAS AF: 0.413

Gnomad4 SAS AF: 0.398

Gnomad4 FIN AF: 0.483

Gnomad4 NFE AF: 0.472

Gnomad4 OTH AF: 0.442

Alfa AF: 0.411 Hom.: 925

Asia WGS AF: 0.334 AC: 1168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.77
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17203612; hg19: chr6-32446853;