rs571296

chr6-116771395-G-Achr6-116771395-G-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 0.308 in 152,070 control chromosomes in the GnomAD database, including 7,976 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 0.31 (7976 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.481 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: 0.308 AC: 46829 AN: 151950 Hom.: 7984 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.497

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.308 AC: 46817 AN: 152070 Hom.: 7976 Cov.: 32 AF XY: 0.305 AC XY: 22692 AN XY: 74346

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.532

Gnomad4 EAS AF: 0.497

Gnomad4 SAS AF: 0.270

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.360

Alfa AF: 0.358 Hom.: 10253

Bravo AF: 0.314

Asia WGS AF: 0.361 AC: 1253 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	7.0
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs571296; hg19: chr6-117092558; COSMIC: COSV69421796;