chr6-18476429-A-G

Variant names:

• chr6-18476429-A-G
• rs532347

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.954

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.909

Gnomad4 FIN AF: 0.971

Gnomad4 NFE AF: 0.951

Gnomad4 OTH AF: 0.918

Alfa AF: 0.945 Hom.: 83230

Bravo AF: 0.918

Asia WGS AF: 0.925 AC: 3218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs532347; hg19: chr6-18476660;