chr6-88014148-C-T

Variant names:

• chr6-88014148-C-T
• rs269434

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 0.882 in 152,194 control chromosomes in the GnomAD database, including 59,360 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 0.88 (59360 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.999
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.887 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.882 AC: 134197 AN: 152076 Hom.: 59328 Cov.: 30

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.850

Gnomad ASJ AF: 0.870

Gnomad EAS AF: 0.792

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.945

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.893

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.882 AC: 134284 AN: 152194 Hom.: 59360 Cov.: 30 AF XY: 0.881 AC XY: 65598 AN XY: 74426

African (AFR) AF: 0.882 AC: 36632 AN: 41514

American (AMR) AF: 0.850 AC: 12988 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.870 AC: 3021 AN: 3472

East Asian (EAS) AF: 0.791 AC: 4090 AN: 5168

South Asian (SAS) AF: 0.789 AC: 3797 AN: 4812

European-Finnish (FIN) AF: 0.945 AC: 10029 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.893 AC: 60753 AN: 68014

Other (OTH) AF: 0.887 AC: 1876 AN: 2114

Alfa AF: 0.887 Hom.: 10791

Bravo AF: 0.876

Asia WGS AF: 0.799 AC: 2779 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	14
DANN	Benign	0.64
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs269434; hg19: chr6-88723866;