chr6-138128418-T-C

Variant names:

• chr6-138128418-T-C
• rs7773257

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 0.134 in 152,210 control chromosomes in the GnomAD database, including 1,451 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 0.13 (1451 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.261 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: 0.134 AC: 20320 AN: 152092 Hom.: 1446 Cov.: 32

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.0586

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.134 AC: 20342 AN: 152210 Hom.: 1451 Cov.: 32 AF XY: 0.133 AC XY: 9875 AN XY: 74418

African (AFR) AF: 0.120 AC: 4993 AN: 41526

American (AMR) AF: 0.117 AC: 1784 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 502 AN: 3470

East Asian (EAS) AF: 0.166 AC: 861 AN: 5176

South Asian (SAS) AF: 0.273 AC: 1315 AN: 4820

European-Finnish (FIN) AF: 0.0586 AC: 622 AN: 10622

Middle Eastern (MID) AF: 0.127 AC: 37 AN: 292

European-Non Finnish (NFE) AF: 0.144 AC: 9811 AN: 67998

Other (OTH) AF: 0.147 AC: 310 AN: 2114

Alfa AF: 0.144 Hom.: 2724

Bravo AF: 0.134

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.1
DANN	Benign	0.50
PhyloP100		0.031

Splicing

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

Other links and lift over

dbSNP: rs7773257; hg19: chr6-138449555;