rs1887244

Variant names:

• chr10-128706642-G-A
• rs1887244

Your query was ambiguous. Multiple possible variants found:

• chr10-128706642-G-A
• chr10-128706642-G-C
• chr10-128706642-G-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 0.893 in 152,188 control chromosomes in the GnomAD database, including 60,852 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 0.89 (60852 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 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: 0.893 AC: 135829 AN: 152070 Hom.: 60789 Cov.: 31

Gnomad AFR AF: 0.911

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.906

Gnomad ASJ AF: 0.833

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.869

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.893 AC: 135952 AN: 152188 Hom.: 60852 Cov.: 31 AF XY: 0.896 AC XY: 66667 AN XY: 74386

Gnomad4 AFR AF: 0.911

Gnomad4 AMR AF: 0.906

Gnomad4 ASJ AF: 0.833

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.901

Gnomad4 NFE AF: 0.869

Gnomad4 OTH AF: 0.885

Alfa AF: 0.872 Hom.: 73038

Bravo AF: 0.893

Asia WGS AF: 0.971 AC: 3373 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.4
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: rs1887244; hg19: chr10-130504906;