chr6-122368255-A-T

Variant names:

• chr6-122368255-A-T
• rs13204990

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 0.404 in 152,098 control chromosomes in the GnomAD database, including 13,142 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 (13142 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 0 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 (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.404 AC: 61413 AN: 151980 Hom.: 13142 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.484

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.404 AC: 61429 AN: 152098 Hom.: 13142 Cov.: 32 AF XY: 0.399 AC XY: 29702 AN XY: 74354

African (AFR) AF: 0.283 AC: 11729 AN: 41502

American (AMR) AF: 0.351 AC: 5368 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1494 AN: 3472

East Asian (EAS) AF: 0.408 AC: 2106 AN: 5160

South Asian (SAS) AF: 0.334 AC: 1611 AN: 4820

European-Finnish (FIN) AF: 0.447 AC: 4729 AN: 10580

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.484 AC: 32902 AN: 67966

Other (OTH) AF: 0.424 AC: 896 AN: 2114

Alfa AF: 0.438 Hom.: 1885

Bravo AF: 0.397

Asia WGS AF: 0.354 AC: 1228 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	0.44
DANN	Benign	0.73
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs13204990; hg19: chr6-122689400;