rs10998035

chr10-68254473-C-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 0.136 in 151,984 control chromosomes in the GnomAD database, including 2,504 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 0.14 (2504 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 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: 0.136 AC: 20672 AN: 151874 Hom.: 2494 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0777

Gnomad ASJ AF: 0.0776

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0326

Gnomad FIN AF: 0.0483

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0707

Gnomad OTH AF: 0.117

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

GnomAD4 genome AF: 0.136 AC: 20699 AN: 151984 Hom.: 2504 Cov.: 32 AF XY: 0.132 AC XY: 9808 AN XY: 74290

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.0775

Gnomad4 ASJ AF: 0.0776

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0324

Gnomad4 FIN AF: 0.0483

Gnomad4 NFE AF: 0.0707

Gnomad4 OTH AF: 0.115

Alfa AF: 0.109 Hom.: 192

Bravo AF: 0.148

Asia WGS AF: 0.0320 AC: 111 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	1.5
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10998035; hg19: chr10-70014230;