rs869244

Variant names:

• chr10-111149347-G-A
• rs869244

Your query was ambiguous. Multiple possible variants found:

• chr10-111149347-G-A
• chr10-111149347-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 0.364 in 151,840 control chromosomes in the GnomAD database, including 10,277 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 0.36 (10277 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.364 AC: 55205 AN: 151722 Hom.: 10235 Cov.: 32

Gnomad AFR AF: 0.362

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.364 AC: 55306 AN: 151840 Hom.: 10277 Cov.: 32 AF XY: 0.364 AC XY: 27047 AN XY: 74240

Gnomad4 AFR AF: 0.362

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.391

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.354

Gnomad4 OTH AF: 0.385

Alfa AF: 0.355 Hom.: 21029

Bravo AF: 0.371

Asia WGS AF: 0.448 AC: 1560 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.6
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs869244; hg19: chr10-112909105;