rs531003

Variant names:

• chr9-110850339-G-C
• rs531003

Your query was ambiguous. Multiple possible variants found:

• chr9-110850339-G-C
• chr9-110850339-G-T

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 0.271 in 151,944 control chromosomes in the GnomAD database, including 5,592 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 0.27 (5592 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.655
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.271 AC: 41184 AN: 151826 Hom.: 5589 Cov.: 32

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.264

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.271 AC: 41230 AN: 151944 Hom.: 5592 Cov.: 32 AF XY: 0.275 AC XY: 20461 AN XY: 74270

African (AFR) AF: 0.282 AC: 11672 AN: 41414

American (AMR) AF: 0.267 AC: 4087 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.264 AC: 917 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1532 AN: 5168

South Asian (SAS) AF: 0.331 AC: 1588 AN: 4804

European-Finnish (FIN) AF: 0.291 AC: 3067 AN: 10546

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.258 AC: 17561 AN: 67946

Other (OTH) AF: 0.257 AC: 542 AN: 2112

Alfa AF: 0.136 Hom.: 240

Bravo AF: 0.265

Asia WGS AF: 0.326 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.82
DANN	Benign	0.66
PhyloP100		-0.66

Splicing

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

Other links and lift over

dbSNP: rs531003; hg19: chr9-113612619;