rs10898290

Positions:

• chr11-71553875-T-C
• chr11-71553875-T-G

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 0.307 in 151,882 control chromosomes in the GnomAD database, including 7,545 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 0.31 (7545 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46670 AN: 151764 Hom.: 7540 Cov.: 31

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.324

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.307 AC: 46703 AN: 151882 Hom.: 7545 Cov.: 31 AF XY: 0.313 AC XY: 23235 AN XY: 74234

Gnomad4 AFR AF: 0.285

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.287

Alfa AF: 0.161 Hom.: 284

Bravo AF: 0.316

Asia WGS AF: 0.325 AC: 1131 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.30
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10898290; hg19: chr11-71264921;