rs2419603

Variant names:

• chr10-112144109-C-T
• rs2419603

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 0.12 in 152,160 control chromosomes in the GnomAD database, including 1,189 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 0.12 (1189 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.464

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.120 AC: 18262 AN: 152042 Hom.: 1185 Cov.: 33

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0822

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.120 AC: 18288 AN: 152160 Hom.: 1189 Cov.: 33 AF XY: 0.119 AC XY: 8848 AN XY: 74382

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.0819

Gnomad4 ASJ AF: 0.0639

Gnomad4 EAS AF: 0.00193

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.117

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.126

Alfa AF: 0.112 Hom.: 1056

Bravo AF: 0.120

Asia WGS AF: 0.0730 AC: 257 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2419603; hg19: chr10-113903867;