rs10187367

Variant names:

• chr2-154465122-G-A
• rs10187367

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 0.0699 in 151,820 control chromosomes in the GnomAD database, including 481 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 0.070 (481 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.183 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: 0.0698 AC: 10596 AN: 151702 Hom.: 480 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0528

Gnomad ASJ AF: 0.0555

Gnomad EAS AF: 0.193

Gnomad SAS AF: 0.0585

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0407

Gnomad OTH AF: 0.0566

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

GnomAD4 genome AF: 0.0699 AC: 10605 AN: 151820 Hom.: 481 Cov.: 31 AF XY: 0.0715 AC XY: 5302 AN XY: 74186

Gnomad4 AFR AF: 0.116

Gnomad4 AMR AF: 0.0527

Gnomad4 ASJ AF: 0.0555

Gnomad4 EAS AF: 0.193

Gnomad4 SAS AF: 0.0594

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.0406

Gnomad4 OTH AF: 0.0560

Alfa AF: 0.0549 Hom.: 51

Bravo AF: 0.0724

Asia WGS AF: 0.108 AC: 377 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10187367; hg19: chr2-155321634;