rs10902173

Variant names:

• chr11-570072-T-C
• rs10902173

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 0.495 in 152,040 control chromosomes in the GnomAD database, including 20,607 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 0.49 (20607 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.63

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.69 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: 0.495 AC: 75219 AN: 151922 Hom.: 20613 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.611

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.710

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.521

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

GnomAD4 genome AF: 0.495 AC: 75218 AN: 152040 Hom.: 20607 Cov.: 32 AF XY: 0.500 AC XY: 37179 AN XY: 74304

Gnomad4 AFR AF: 0.243

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.710

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.519

Alfa AF: 0.512 Hom.: 3959

Bravo AF: 0.470

Asia WGS AF: 0.591 AC: 2057 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	0.32
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10902173; hg19: chr11-570072;