chr6-96756418-C-A

Variant names:

• chr6-96756418-C-A
• rs11153162

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 0.172 in 151,618 control chromosomes in the GnomAD database, including 2,471 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 0.17 (2471 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.2 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: 0.172 AC: 26031 AN: 151500 Hom.: 2469 Cov.: 32

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.00174

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.172 AC: 26038 AN: 151618 Hom.: 2471 Cov.: 32 AF XY: 0.170 AC XY: 12617 AN XY: 74114

African (AFR) AF: 0.128 AC: 5290 AN: 41370

American (AMR) AF: 0.166 AC: 2526 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3466

East Asian (EAS) AF: 0.00174 AC: 9 AN: 5168

South Asian (SAS) AF: 0.120 AC: 577 AN: 4824

European-Finnish (FIN) AF: 0.245 AC: 2540 AN: 10348

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13738 AN: 67874

Other (OTH) AF: 0.181 AC: 382 AN: 2110

Alfa AF: 0.181 Hom.: 2049

Bravo AF: 0.166

Asia WGS AF: 0.0690 AC: 239 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	8.2
DANN	Benign	0.83
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs11153162; hg19: chr6-97204294;