rs6938397

Variant names:

• chr6-27263445-C-G
• rs6938397

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 0.126 in 152,188 control chromosomes in the GnomAD database, including 1,402 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 (1402 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 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: 0.126 AC: 19213 AN: 152070 Hom.: 1403 Cov.: 33

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.0938

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0776

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.126 AC: 19218 AN: 152188 Hom.: 1402 Cov.: 33 AF XY: 0.130 AC XY: 9666 AN XY: 74404

African (AFR) AF: 0.161 AC: 6667 AN: 41514

American (AMR) AF: 0.0936 AC: 1432 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3472

East Asian (EAS) AF: 0.115 AC: 596 AN: 5176

South Asian (SAS) AF: 0.0783 AC: 378 AN: 4826

European-Finnish (FIN) AF: 0.222 AC: 2349 AN: 10578

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7114 AN: 68006

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.112 Hom.: 109

Bravo AF: 0.120

Asia WGS AF: 0.0840 AC: 292 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.4
DANN	Benign	0.43
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs6938397; hg19: chr6-27231224;