rs2861442

Positions:

• chr10-44389511-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;