rs869244

chr10-111149347-G-Achr10-111149347-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;