10-121367248-A-G

Variant names:

• chr10-121367248-A-G
• rs10510093

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 0.307 in 152,190 control chromosomes in the GnomAD database, including 7,984 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 0.31 (7984 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.274
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 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: 0.308 AC: 46790 AN: 152070 Hom.: 7984 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.373

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.383

Gnomad EAS AF: 0.323

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.307 AC: 46793 AN: 152190 Hom.: 7984 Cov.: 33 AF XY: 0.307 AC XY: 22828 AN XY: 74420

African (AFR) AF: 0.153 AC: 6340 AN: 41536

American (AMR) AF: 0.274 AC: 4197 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.383 AC: 1330 AN: 3472

East Asian (EAS) AF: 0.323 AC: 1669 AN: 5174

South Asian (SAS) AF: 0.297 AC: 1432 AN: 4826

European-Finnish (FIN) AF: 0.380 AC: 4023 AN: 10578

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.393 AC: 26712 AN: 67990

Other (OTH) AF: 0.315 AC: 664 AN: 2108

Alfa AF: 0.324 Hom.: 1077

Bravo AF: 0.292

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.34
DANN	Benign	0.45
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10510093; hg19: chr10-123126762;