rs2386638

Variant names:

• chr10-5667884-G-C
• rs2386638

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 0.26 in 152,098 control chromosomes in the GnomAD database, including 5,329 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 0.26 (5329 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.326 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: 0.260 AC: 39501 AN: 151980 Hom.: 5320 Cov.: 33

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.260 AC: 39545 AN: 152098 Hom.: 5329 Cov.: 33 AF XY: 0.263 AC XY: 19548 AN XY: 74350

Gnomad4 AFR AF: 0.294

Gnomad4 AMR AF: 0.188

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.270

Alfa AF: 0.269 Hom.: 662

Bravo AF: 0.250

Asia WGS AF: 0.206 AC: 718 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2386638; hg19: chr10-5709847;