rs10998624

Positions:

• chr10-69180045-G-A
• chr10-69180045-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 0.11 in 152,230 control chromosomes in the GnomAD database, including 2,296 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 0.11 (2296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.32 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: 0.110 AC: 16730 AN: 152112 Hom.: 2281 Cov.: 32

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0609

Gnomad ASJ AF: 0.0547

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0730

Gnomad FIN AF: 0.00594

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0151

Gnomad OTH AF: 0.0908

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

GnomAD4 genome AF: 0.110 AC: 16786 AN: 152230 Hom.: 2296 Cov.: 32 AF XY: 0.108 AC XY: 8010 AN XY: 74442

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.0608

Gnomad4 ASJ AF: 0.0547

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0726

Gnomad4 FIN AF: 0.00594

Gnomad4 NFE AF: 0.0151

Gnomad4 OTH AF: 0.0913

Alfa AF: 0.0259 Hom.: 431

Bravo AF: 0.123

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	3.8
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10998624; hg19: chr10-70939801;