6-125769231-T-C

Variant names:

• chr6-125769231-T-C
• rs9388451

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 0.405 in 152,046 control chromosomes in the GnomAD database, including 14,174 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 0.41 (14174 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49
• Publications: 50 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.681 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: 0.405 AC: 61576 AN: 151928 Hom.: 14160 Cov.: 31

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.405 AC: 61598 AN: 152046 Hom.: 14174 Cov.: 31 AF XY: 0.405 AC XY: 30067 AN XY: 74306

African (AFR) AF: 0.169 AC: 7015 AN: 41490

American (AMR) AF: 0.462 AC: 7058 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1333 AN: 3466

East Asian (EAS) AF: 0.700 AC: 3618 AN: 5168

South Asian (SAS) AF: 0.414 AC: 1992 AN: 4816

European-Finnish (FIN) AF: 0.487 AC: 5138 AN: 10540

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.501 AC: 34043 AN: 67970

Other (OTH) AF: 0.452 AC: 955 AN: 2112

Alfa AF: 0.460 Hom.: 26062

Bravo AF: 0.399

Asia WGS AF: 0.533 AC: 1851 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	13
DANN	Benign	0.77
PhyloP100		2.5

Splicing

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

Other links and lift over

dbSNP: rs9388451; hg19: chr6-126090377;