rs17061461

Positions:

• chr6-132571865-T-C

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 0.049 in 152,172 control chromosomes in the GnomAD database, including 260 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 0.049 (260 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0490 AC: 7450 AN: 152054 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.0736

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.0238

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0279

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0490 AC: 7461 AN: 152172 Hom.: 260 Cov.: 32 AF XY: 0.0495 AC XY: 3682 AN XY: 74406

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.0582

Gnomad4 ASJ AF: 0.0484

Gnomad4 EAS AF: 0.162

Gnomad4 SAS AF: 0.0238

Gnomad4 FIN AF: 0.0360

Gnomad4 NFE AF: 0.0279

Gnomad4 OTH AF: 0.0489

Alfa AF: 0.0402 Hom.: 23

Bravo AF: 0.0549

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.58
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17061461; hg19: chr6-132893004;