rs10192369

Variant names:

• chr2-160524377-G-A
• rs10192369

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.265 AC: 10997 AN: 41434

American (AMR) AF: 0.624 AC: 9503 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.514 AC: 1783 AN: 3466

East Asian (EAS) AF: 0.688 AC: 3555 AN: 5164

South Asian (SAS) AF: 0.579 AC: 2780 AN: 4804

European-Finnish (FIN) AF: 0.513 AC: 5408 AN: 10538

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.499 AC: 33902 AN: 67954

Other (OTH) AF: 0.507 AC: 1072 AN: 2114

Alfa AF: 0.499 Hom.: 87443

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
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs10192369; hg19: chr2-161380888;