rs9550637

Variant names:

• chr13-20338388-A-G
• rs9550637

Your query was ambiguous. Multiple possible variants found:

• chr13-20338388-A-G
• chr13-20338388-A-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 0.317 in 152,104 control chromosomes in the GnomAD database, including 8,700 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 0.32 (8700 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.71
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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: 0.317 AC: 48251 AN: 151986 Hom.: 8710 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.370

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.317 AC: 48239 AN: 152104 Hom.: 8700 Cov.: 32 AF XY: 0.326 AC XY: 24255 AN XY: 74346

African (AFR) AF: 0.181 AC: 7515 AN: 41510

American (AMR) AF: 0.310 AC: 4734 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.436 AC: 1511 AN: 3468

East Asian (EAS) AF: 0.732 AC: 3789 AN: 5174

South Asian (SAS) AF: 0.368 AC: 1771 AN: 4810

European-Finnish (FIN) AF: 0.435 AC: 4591 AN: 10566

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.341 AC: 23208 AN: 67974

Other (OTH) AF: 0.320 AC: 674 AN: 2106

Alfa AF: 0.338 Hom.: 38736

Bravo AF: 0.305

Asia WGS AF: 0.459 AC: 1596 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.23
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs9550637; hg19: chr13-20912527;