rs9501030

Variant names:

• chr6-30831622-T-A
• rs9501030

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 0.201 in 152,104 control chromosomes in the GnomAD database, including 3,640 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 0.20 (3640 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.334
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.431 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: 0.201 AC: 30607 AN: 151986 Hom.: 3624 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.201 AC: 30641 AN: 152104 Hom.: 3640 Cov.: 32 AF XY: 0.210 AC XY: 15591 AN XY: 74366

African (AFR) AF: 0.154 AC: 6413 AN: 41508

American (AMR) AF: 0.314 AC: 4803 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 829 AN: 3466

East Asian (EAS) AF: 0.394 AC: 2033 AN: 5158

South Asian (SAS) AF: 0.446 AC: 2150 AN: 4816

European-Finnish (FIN) AF: 0.197 AC: 2087 AN: 10586

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11513 AN: 67978

Other (OTH) AF: 0.225 AC: 476 AN: 2112

Alfa AF: 0.180 Hom.: 367

Bravo AF: 0.203

Asia WGS AF: 0.488 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.8
DANN	Benign	0.76
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs9501030; hg19: chr6-30799399;