rs10998035

Variant names:

• chr10-68254473-C-T
• rs10998035

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.323 AC: 13374 AN: 41388

American (AMR) AF: 0.0775 AC: 1183 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0776 AC: 269 AN: 3468

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5176

South Asian (SAS) AF: 0.0324 AC: 156 AN: 4810

European-Finnish (FIN) AF: 0.0483 AC: 511 AN: 10574

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0707 AC: 4805 AN: 67986

Other (OTH) AF: 0.115 AC: 244 AN: 2114

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
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10998035; hg19: chr10-70014230;