2-233916448-T-C

Variant names:

• chr2-233916448-T-C
• rs10166942

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 0.399 in 152,076 control chromosomes in the GnomAD database, including 17,691 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 0.40 (17691 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0610

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.795 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: 0.399 AC: 60623 AN: 151958 Hom.: 17643 Cov.: 32

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.399 AC: 60736 AN: 152076 Hom.: 17691 Cov.: 32 AF XY: 0.399 AC XY: 29683 AN XY: 74342

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.647

Gnomad4 SAS AF: 0.441

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.195

Gnomad4 OTH AF: 0.346

Alfa AF: 0.233 Hom.: 8198

Bravo AF: 0.428

Asia WGS AF: 0.600 AC: 2086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10166942; hg19: chr2-234825093;