chr10-9133493-G-A

Variant names:

• chr10-9133493-G-A
• rs10508402

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 0.0305 in 129,862 control chromosomes in the GnomAD database, including 141 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 0.030 (141 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.11 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: 0.0304 AC: 3940 AN: 129784 Hom.: 137 Cov.: 31

Gnomad AFR AF: 0.00789

Gnomad AMI AF: 0.00489

Gnomad AMR AF: 0.114

Gnomad ASJ AF: 0.00561

Gnomad EAS AF: 0.00306

Gnomad SAS AF: 0.0167

Gnomad FIN AF: 0.0288

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0288

Gnomad OTH AF: 0.0265

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

GnomAD4 genome AF: 0.0305 AC: 3956 AN: 129862 Hom.: 141 Cov.: 31 AF XY: 0.0323 AC XY: 2053 AN XY: 63616

African (AFR) AF: 0.00787 AC: 249 AN: 31658

American (AMR) AF: 0.115 AC: 1545 AN: 13480

Ashkenazi Jewish (ASJ) AF: 0.00561 AC: 17 AN: 3030

East Asian (EAS) AF: 0.00307 AC: 15 AN: 4888

South Asian (SAS) AF: 0.0169 AC: 74 AN: 4380

European-Finnish (FIN) AF: 0.0288 AC: 265 AN: 9200

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 246

European-Non Finnish (NFE) AF: 0.0288 AC: 1740 AN: 60364

Other (OTH) AF: 0.0261 AC: 47 AN: 1798

Alfa AF: 0.0261 Hom.: 12

Bravo AF: 0.0312

Asia WGS AF: 0.0120 AC: 40 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	3.3
DANN	Benign	0.61
PhyloP100		-0.0060

Splicing

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

Other links and lift over

dbSNP: rs10508402; hg19: chr10-9175456;