rs10192369

Variant names:

• chr2-160524377-G-A
• rs10192369

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 0.458 in 151,912 control chromosomes in the GnomAD database, including 17,461 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 0.46 (17461 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.722

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.67 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: 0.458 AC: 69595 AN: 151794 Hom.: 17439 Cov.: 31

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.688

Gnomad SAS AF: 0.577

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.499

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.458 AC: 69645 AN: 151912 Hom.: 17461 Cov.: 31 AF XY: 0.467 AC XY: 34648 AN XY: 74220

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.624

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.579

Gnomad4 FIN AF: 0.513

Gnomad4 NFE AF: 0.499

Gnomad4 OTH AF: 0.507

Alfa AF: 0.512 Hom.: 45926

Bravo AF: 0.463

Asia WGS AF: 0.572 AC: 1984 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.2
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10192369; hg19: chr2-161380888;