rs10509054

Variant names:

• chr10-56655936-G-T
• rs10509054

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 0.0387 in 152,122 control chromosomes in the GnomAD database, including 131 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 0.039 (131 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 2 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 = 0.0552 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: 0.0386 AC: 5872 AN: 152002 Hom.: 131 Cov.: 32

Gnomad AFR AF: 0.0296

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0350

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0609

Gnomad FIN AF: 0.0323

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0467

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0387 AC: 5880 AN: 152122 Hom.: 131 Cov.: 32 AF XY: 0.0382 AC XY: 2841 AN XY: 74372

African (AFR) AF: 0.0297 AC: 1232 AN: 41466

American (AMR) AF: 0.0350 AC: 534 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0524 AC: 182 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.0610 AC: 294 AN: 4822

European-Finnish (FIN) AF: 0.0323 AC: 343 AN: 10604

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0467 AC: 3176 AN: 68000

Other (OTH) AF: 0.0417 AC: 88 AN: 2112

Alfa AF: 0.0396 Hom.: 13

Bravo AF: 0.0380

Asia WGS AF: 0.0240 AC: 83 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.17
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs10509054; hg19: chr10-58415696;