6-34231315-C-T

Variant names:

• chr6-34231315-C-T
• rs2780226

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 0.801 in 152,188 control chromosomes in the GnomAD database, including 50,560 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 0.80 (50560 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.78
• Publications: 58 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.915 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: 0.801 AC: 121798 AN: 152070 Hom.: 50558 Cov.: 34

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.787

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

GnomAD4 genome AF: 0.801 AC: 121834 AN: 152188 Hom.: 50560 Cov.: 34 AF XY: 0.804 AC XY: 59835 AN XY: 74416

African (AFR) AF: 0.577 AC: 23953 AN: 41486

American (AMR) AF: 0.722 AC: 11034 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2920 AN: 3472

East Asian (EAS) AF: 0.880 AC: 4559 AN: 5182

South Asian (SAS) AF: 0.938 AC: 4510 AN: 4808

European-Finnish (FIN) AF: 0.952 AC: 10107 AN: 10614

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 62055 AN: 68020

Other (OTH) AF: 0.788 AC: 1668 AN: 2116

Alfa AF: 0.876 Hom.: 182070

Bravo AF: 0.768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.53
DANN	Benign	0.81
PhyloP100		-3.8

Splicing

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

Other links and lift over

dbSNP: rs2780226; hg19: chr6-34199092;