rs2380205

Variant names:

• chr10-5844771-C-T
• rs2380205

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 0.456 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
• Publications: 107 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.596 AC: 24733 AN: 41494

American (AMR) AF: 0.368 AC: 5628 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1076 AN: 3470

East Asian (EAS) AF: 0.119 AC: 616 AN: 5188

South Asian (SAS) AF: 0.259 AC: 1250 AN: 4828

European-Finnish (FIN) AF: 0.440 AC: 4652 AN: 10576

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29894 AN: 67964

Other (OTH) AF: 0.468 AC: 990 AN: 2116

Alfa AF: 0.431 Hom.: 44045

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
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs2380205; hg19: chr10-5886734;