rs10933595

Variant names:

• chr2-240352405-G-A
• rs10933595

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.503 in 152,074 control chromosomes in the GnomAD database, including 20,237 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 0.50 (20237 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.30

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.592 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: 0.503 AC: 76449 AN: 151956 Hom.: 20237 Cov.: 34

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.550

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

GnomAD4 genome AF: 0.503 AC: 76481 AN: 152074 Hom.: 20237 Cov.: 34 AF XY: 0.497 AC XY: 36937 AN XY: 74320

Gnomad4 AFR AF: 0.346

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.384

Gnomad4 SAS AF: 0.369

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.545

Alfa AF: 0.577 Hom.: 33779

Bravo AF: 0.498

Asia WGS AF: 0.365 AC: 1267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10933595; hg19: chr2-241291822;