chr9-5213687-T-C

Variant names:

• chr9-5213687-T-C
• rs10975003

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 0.427 in 152,042 control chromosomes in the GnomAD database, including 15,522 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 0.43 (15522 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.380
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.648 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: 0.427 AC: 64860 AN: 151924 Hom.: 15491 Cov.: 33

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.348

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.400

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.427 AC: 64943 AN: 152042 Hom.: 15522 Cov.: 33 AF XY: 0.426 AC XY: 31651 AN XY: 74302

African (AFR) AF: 0.655 AC: 27141 AN: 41452

American (AMR) AF: 0.382 AC: 5832 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.348 AC: 1208 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1172 AN: 5174

South Asian (SAS) AF: 0.401 AC: 1929 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3947 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.330 AC: 22461 AN: 67974

Other (OTH) AF: 0.414 AC: 875 AN: 2112

Alfa AF: 0.362 Hom.: 36382

Bravo AF: 0.433

Asia WGS AF: 0.339 AC: 1178 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.0
DANN	Benign	0.85
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs10975003; hg19: chr9-5213687; COSMIC: COSV60323593;