6-18476429-A-G

Variant names:

• chr6-18476429-A-G
• rs532347

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 0.923 in 152,276 control chromosomes in the GnomAD database, including 65,012 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 0.92 (65012 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.383
• Publications: 1 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 (EAS) allele frequency at 95% confidence interval = 0.947 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: 0.923 AC: 140455 AN: 152158 Hom.: 64966 Cov.: 32

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.979

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.954

Gnomad EAS AF: 0.969

Gnomad SAS AF: 0.909

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.923 AC: 140559 AN: 152276 Hom.: 65012 Cov.: 32 AF XY: 0.924 AC XY: 68772 AN XY: 74460

African (AFR) AF: 0.858 AC: 35631 AN: 41530

American (AMR) AF: 0.920 AC: 14087 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.954 AC: 3314 AN: 3472

East Asian (EAS) AF: 0.969 AC: 5015 AN: 5174

South Asian (SAS) AF: 0.909 AC: 4387 AN: 4824

European-Finnish (FIN) AF: 0.971 AC: 10317 AN: 10622

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64695 AN: 68030

Other (OTH) AF: 0.918 AC: 1940 AN: 2114

Alfa AF: 0.941 Hom.: 195556

Bravo AF: 0.918

Asia WGS AF: 0.925 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.71
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs532347; hg19: chr6-18476660;