rs2666236

chr10-33129944-G-Achr10-33129944-G-C

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 0.501 in 151,922 control chromosomes in the GnomAD database, including 19,842 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 (19842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.501 AC: 76023 AN: 151804 Hom.: 19818 Cov.: 32

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.399

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.526

Gnomad EAS AF: 0.752

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.501 AC: 76086 AN: 151922 Hom.: 19842 Cov.: 32 AF XY: 0.500 AC XY: 37165 AN XY: 74258

Gnomad4 AFR AF: 0.613

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.526

Gnomad4 EAS AF: 0.751

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.514

Alfa AF: 0.456 Hom.: 3222

Bravo AF: 0.516

Asia WGS AF: 0.642 AC: 2234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	6.8
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2666236; hg19: chr10-33418872;