6-34227234-G-T

Variant names:

• chr6-34227234-G-T
• rs1776897

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 0.8 in 152,002 control chromosomes in the GnomAD database, including 50,447 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 (50447 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 64 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.919 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: 0.800 AC: 121542 AN: 151884 Hom.: 50445 Cov.: 30

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.843

Gnomad AMR AF: 0.722

Gnomad ASJ AF: 0.841

Gnomad EAS AF: 0.879

Gnomad SAS AF: 0.941

Gnomad FIN AF: 0.952

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.912

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.800 AC: 121578 AN: 152002 Hom.: 50447 Cov.: 30 AF XY: 0.803 AC XY: 59711 AN XY: 74318

African (AFR) AF: 0.574 AC: 23779 AN: 41396

American (AMR) AF: 0.722 AC: 11019 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.841 AC: 2917 AN: 3470

East Asian (EAS) AF: 0.880 AC: 4534 AN: 5154

South Asian (SAS) AF: 0.941 AC: 4538 AN: 4820

European-Finnish (FIN) AF: 0.952 AC: 10112 AN: 10618

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.912 AC: 61992 AN: 67962

Other (OTH) AF: 0.789 AC: 1662 AN: 2106

Alfa AF: 0.874 Hom.: 172063

Bravo AF: 0.767

Asia WGS AF: 0.860 AC: 2990 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.77
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1776897; hg19: chr6-34195011;