rs6841268

Variant names:

• chr4-138247487-A-T
• rs6841268

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 0.402 in 151,542 control chromosomes in the GnomAD database, including 13,099 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 0.40 (13099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.565
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.497 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: 0.402 AC: 60906 AN: 151424 Hom.: 13092 Cov.: 31

Gnomad AFR AF: 0.261

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.514

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.402 AC: 60935 AN: 151542 Hom.: 13099 Cov.: 31 AF XY: 0.399 AC XY: 29542 AN XY: 74052

African (AFR) AF: 0.261 AC: 10814 AN: 41412

American (AMR) AF: 0.388 AC: 5922 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1461 AN: 3456

East Asian (EAS) AF: 0.313 AC: 1619 AN: 5168

South Asian (SAS) AF: 0.514 AC: 2476 AN: 4816

European-Finnish (FIN) AF: 0.424 AC: 4382 AN: 10346

Middle Eastern (MID) AF: 0.476 AC: 139 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32772 AN: 67792

Other (OTH) AF: 0.410 AC: 861 AN: 2100

Alfa AF: 0.433 Hom.: 1852

Bravo AF: 0.390

Asia WGS AF: 0.418 AC: 1438 AN: 3440

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.66
DANN	Benign	0.57
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs6841268; hg19: chr4-139168641;