6-121018033-A-G

Variant names:

• chr6-121018033-A-G
• rs1343075

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 0.146 in 151,938 control chromosomes in the GnomAD database, including 2,530 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 0.15 (2530 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.575 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22141 AN: 151820 Hom.: 2527 Cov.: 31

Gnomad AFR AF: 0.0514

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.594

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.196

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.146 AC: 22154 AN: 151938 Hom.: 2530 Cov.: 31 AF XY: 0.152 AC XY: 11303 AN XY: 74258

African (AFR) AF: 0.0514 AC: 2133 AN: 41488

American (AMR) AF: 0.146 AC: 2227 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3055 AN: 5152

South Asian (SAS) AF: 0.329 AC: 1584 AN: 4818

European-Finnish (FIN) AF: 0.196 AC: 2077 AN: 10572

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9667 AN: 67900

Other (OTH) AF: 0.169 AC: 354 AN: 2098

Alfa AF: 0.149 Hom.: 5161

Bravo AF: 0.137

Asia WGS AF: 0.403 AC: 1399 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.66
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1343075; hg19: chr6-121339179; COSMIC: COSV60276406;