rs2861442

Variant names:

• chr10-44389511-T-C
• rs2861442

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 0.253 in 152,054 control chromosomes in the GnomAD database, including 5,053 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 0.25 (5053 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 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: 0.253 AC: 38446 AN: 151938 Hom.: 5053 Cov.: 32

Gnomad AFR AF: 0.225

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0967

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.287

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.253 AC: 38451 AN: 152054 Hom.: 5053 Cov.: 32 AF XY: 0.249 AC XY: 18506 AN XY: 74312

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0970

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.287

Gnomad4 NFE AF: 0.295

Gnomad4 OTH AF: 0.265

Alfa AF: 0.273 Hom.: 2759

Bravo AF: 0.248

Asia WGS AF: 0.106 AC: 370 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.1
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2861442; hg19: chr10-44884959;