chr6-104051246-C-A

Variant names:

• chr6-104051246-C-A
• rs9404502

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 0.135 in 151,854 control chromosomes in the GnomAD database, including 1,524 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 (1524 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.184 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: 0.135 AC: 20542 AN: 151738 Hom.: 1519 Cov.: 32

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.0635

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.135 AC: 20555 AN: 151854 Hom.: 1524 Cov.: 32 AF XY: 0.133 AC XY: 9863 AN XY: 74224

African (AFR) AF: 0.0910 AC: 3772 AN: 41448

American (AMR) AF: 0.190 AC: 2881 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3464

East Asian (EAS) AF: 0.152 AC: 781 AN: 5138

South Asian (SAS) AF: 0.178 AC: 857 AN: 4820

European-Finnish (FIN) AF: 0.0635 AC: 671 AN: 10570

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10512 AN: 67898

Other (OTH) AF: 0.171 AC: 362 AN: 2112

Alfa AF: 0.155 Hom.: 5326

Bravo AF: 0.142

Asia WGS AF: 0.147 AC: 513 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	8.1
DANN	Benign	0.53
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs9404502; hg19: chr6-104499121;