rs2380205

chr10-5844771-C-T

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 0.456 in 152,116 control chromosomes in the GnomAD database, including 16,911 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 (16911 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.652

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.59 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: 0.456 AC: 69346 AN: 151998 Hom.: 16891 Cov.: 33

Gnomad AFR AF: 0.596

Gnomad AMI AF: 0.472

Gnomad AMR AF: 0.369

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.456 AC: 69415 AN: 152116 Hom.: 16911 Cov.: 33 AF XY: 0.449 AC XY: 33381 AN XY: 74376

Gnomad4 AFR AF: 0.596

Gnomad4 AMR AF: 0.368

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.440

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.468

Alfa AF: 0.415 Hom.: 15712

Bravo AF: 0.458

Asia WGS AF: 0.307 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.3
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2380205; hg19: chr10-5886734;