rs571296

Variant names:

• chr6-116771395-G-A
• rs571296

Your query was ambiguous. Multiple possible variants found:

• chr6-116771395-G-A
• chr6-116771395-G-C

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 0.308 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
• Publications: 9 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.183 AC: 7599 AN: 41486

American (AMR) AF: 0.355 AC: 5420 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1848 AN: 3472

East Asian (EAS) AF: 0.497 AC: 2575 AN: 5176

South Asian (SAS) AF: 0.270 AC: 1302 AN: 4822

European-Finnish (FIN) AF: 0.265 AC: 2800 AN: 10558

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23934 AN: 67974

Other (OTH) AF: 0.360 AC: 760 AN: 2112

Alfa AF: 0.350 Hom.: 12857

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
PhyloP100		0.47

Splicing

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

Other links and lift over

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