chr6-135106006-C-A

Variant names:

• chr6-135106006-C-A
• rs9376092

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 0.244 in 151,960 control chromosomes in the GnomAD database, including 4,840 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 0.24 (4840 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0920
• Publications: 59 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.268 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37060 AN: 151842 Hom.: 4834 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.279

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.244 AC: 37074 AN: 151960 Hom.: 4840 Cov.: 32 AF XY: 0.243 AC XY: 18056 AN XY: 74236

African (AFR) AF: 0.199 AC: 8244 AN: 41458

American (AMR) AF: 0.215 AC: 3291 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 824 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1441 AN: 5150

South Asian (SAS) AF: 0.111 AC: 534 AN: 4818

European-Finnish (FIN) AF: 0.349 AC: 3671 AN: 10532

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.270 AC: 18372 AN: 67934

Other (OTH) AF: 0.218 AC: 460 AN: 2108

Alfa AF: 0.262 Hom.: 25132

Bravo AF: 0.237

Asia WGS AF: 0.178 AC: 619 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.29
PhyloP100		0.092

Splicing

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

Other links and lift over

dbSNP: rs9376092; hg19: chr6-135427144; COSMIC: COSV73231457;