2-67738865-C-T

Variant names:

• chr2-67738865-C-T
• rs10519124

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 0.103 in 152,252 control chromosomes in the GnomAD database, including 962 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 0.10 (962 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.906

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 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: 0.103 AC: 15626 AN: 152134 Hom.: 962 Cov.: 33

Gnomad AFR AF: 0.0324

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.103 AC: 15632 AN: 152252 Hom.: 962 Cov.: 33 AF XY: 0.103 AC XY: 7656 AN XY: 74450

Gnomad4 AFR AF: 0.0323

Gnomad4 AMR AF: 0.119

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0958

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.135

Alfa AF: 0.134 Hom.: 2805

Bravo AF: 0.101

Asia WGS AF: 0.104 AC: 363 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	9.2
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519124; hg19: chr2-67965997;