rs571060

Positions:

• chr6-111975317-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 0.0867 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.0556

Gnomad4 ASJ AF: 0.0663

Gnomad4 EAS AF: 0.00771

Gnomad4 SAS AF: 0.0568

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.0315

Gnomad4 OTH AF: 0.0877

Alfa AF: 0.0574 Hom.: 194

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs571060; hg19: chr6-112296520;