chr6-92962771-C-G

Variant names:

• chr6-92962771-C-G
• rs2506960

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 0.162 in 151,920 control chromosomes in the GnomAD database, including 4,362 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 0.16 (4362 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24603 AN: 151804 Hom.: 4360 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.0310

Gnomad MID AF: 0.157

Gnomad NFE AF: 0.0190

Gnomad OTH AF: 0.161

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

GnomAD4 genome AF: 0.162 AC: 24638 AN: 151920 Hom.: 4362 Cov.: 32 AF XY: 0.168 AC XY: 12498 AN XY: 74254

African (AFR) AF: 0.345 AC: 14296 AN: 41402

American (AMR) AF: 0.212 AC: 3227 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3468

East Asian (EAS) AF: 0.708 AC: 3651 AN: 5156

South Asian (SAS) AF: 0.195 AC: 940 AN: 4814

European-Finnish (FIN) AF: 0.0310 AC: 328 AN: 10594

Middle Eastern (MID) AF: 0.162 AC: 47 AN: 290

European-Non Finnish (NFE) AF: 0.0190 AC: 1291 AN: 67928

Other (OTH) AF: 0.164 AC: 345 AN: 2110

Alfa AF: 0.0225 Hom.: 39

Bravo AF: 0.188

Asia WGS AF: 0.402 AC: 1392 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.8
DANN	Benign	0.79
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2506960; hg19: chr6-93672489;