chr6-130506337-C-T

Variant names:

• chr6-130506337-C-T
• rs9402234

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 0.144 in 151,980 control chromosomes in the GnomAD database, including 1,826 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 0.14 (1826 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 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: 0.144 AC: 21875 AN: 151862 Hom.: 1811 Cov.: 31

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0821

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.100

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.144 AC: 21926 AN: 151980 Hom.: 1826 Cov.: 31 AF XY: 0.145 AC XY: 10799 AN XY: 74270

African (AFR) AF: 0.201 AC: 8344 AN: 41414

American (AMR) AF: 0.171 AC: 2611 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.158 AC: 547 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1645 AN: 5176

South Asian (SAS) AF: 0.142 AC: 683 AN: 4820

European-Finnish (FIN) AF: 0.0821 AC: 867 AN: 10558

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.100 AC: 6824 AN: 67972

Other (OTH) AF: 0.155 AC: 327 AN: 2110

Alfa AF: 0.109 Hom.: 1162

Bravo AF: 0.156

Asia WGS AF: 0.260 AC: 905 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	8.3
DANN	Benign	0.80
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs9402234; hg19: chr6-130827482;