rs17061461

Variant names:

• chr6-132571865-T-C
• rs17061461

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 0.049 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0736 AC: 3055 AN: 41518

American (AMR) AF: 0.0582 AC: 890 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3472

East Asian (EAS) AF: 0.162 AC: 839 AN: 5168

South Asian (SAS) AF: 0.0238 AC: 115 AN: 4830

European-Finnish (FIN) AF: 0.0360 AC: 382 AN: 10606

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0279 AC: 1897 AN: 67980

Other (OTH) AF: 0.0489 AC: 103 AN: 2108

Alfa AF: 0.0359 Hom.: 71

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs17061461; hg19: chr6-132893004;