rs17061446

Variant names:

• chr6-132570037-G-A
• rs17061446

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 0.0726 in 152,050 control chromosomes in the GnomAD database, including 426 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 0.073 (426 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0786 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: 0.0726 AC: 11030 AN: 151932 Hom.: 425 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.0819

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.0303

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0677

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0804

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0726 AC: 11040 AN: 152050 Hom.: 426 Cov.: 32 AF XY: 0.0707 AC XY: 5252 AN XY: 74298

Gnomad4 AFR AF: 0.0709

Gnomad4 AMR AF: 0.0817

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.0304

Gnomad4 SAS AF: 0.0185

Gnomad4 FIN AF: 0.0677

Gnomad4 NFE AF: 0.0804

Gnomad4 OTH AF: 0.0771

Alfa AF: 0.0786 Hom.: 54

Bravo AF: 0.0767

Asia WGS AF: 0.0280 AC: 96 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17061446; hg19: chr6-132891176;