rs571060

Variant names:

• chr6-111975317-T-C
• rs571060

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 0.0867 in 152,244 control chromosomes in the GnomAD database, including 1,159 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 0.087 (1159 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.47
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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: 0.0864 AC: 13146 AN: 152126 Hom.: 1147 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0557

Gnomad ASJ AF: 0.0663

Gnomad EAS AF: 0.00769

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0315

Gnomad OTH AF: 0.0838

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

GnomAD4 genome AF: 0.0867 AC: 13193 AN: 152244 Hom.: 1159 Cov.: 32 AF XY: 0.0851 AC XY: 6332 AN XY: 74436

African (AFR) AF: 0.224 AC: 9295 AN: 41494

American (AMR) AF: 0.0556 AC: 851 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0663 AC: 230 AN: 3468

East Asian (EAS) AF: 0.00771 AC: 40 AN: 5188

South Asian (SAS) AF: 0.0568 AC: 274 AN: 4828

European-Finnish (FIN) AF: 0.0138 AC: 147 AN: 10632

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0315 AC: 2142 AN: 68018

Other (OTH) AF: 0.0877 AC: 185 AN: 2110

Alfa AF: 0.0606 Hom.: 248

Bravo AF: 0.0949

Asia WGS AF: 0.0640 AC: 221 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.032
DANN	Benign	0.61
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs571060; hg19: chr6-112296520;