chr6-130553304-A-T

Variant names:

• chr6-130553304-A-T
• rs1203350

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 0.516 in 152,104 control chromosomes in the GnomAD database, including 21,372 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 0.52 (21372 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.746 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: 0.516 AC: 78451 AN: 151984 Hom.: 21344 Cov.: 33

Gnomad AFR AF: 0.662

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.516 AC: 78532 AN: 152104 Hom.: 21372 Cov.: 33 AF XY: 0.522 AC XY: 38802 AN XY: 74350

African (AFR) AF: 0.662 AC: 27443 AN: 41472

American (AMR) AF: 0.478 AC: 7305 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1807 AN: 3472

East Asian (EAS) AF: 0.766 AC: 3960 AN: 5170

South Asian (SAS) AF: 0.638 AC: 3075 AN: 4820

European-Finnish (FIN) AF: 0.449 AC: 4758 AN: 10594

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28628 AN: 67978

Other (OTH) AF: 0.526 AC: 1111 AN: 2114

Alfa AF: 0.477 Hom.: 2203

Bravo AF: 0.522

Asia WGS AF: 0.703 AC: 2445 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	4.9
DANN	Benign	0.58
PhyloP100		0.64

Splicing

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

Other links and lift over

dbSNP: rs1203350; hg19: chr6-130874449; COSMIC: COSV69426277;