10-42998449-C-T

Position:

• chr10-42998449-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 0.148 in 152,190 control chromosomes in the GnomAD database, including 1,991 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 0.15 (1991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.341 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: 0.148 AC: 22561 AN: 152072 Hom.: 1988 Cov.: 32

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.134

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.148 AC: 22588 AN: 152190 Hom.: 1991 Cov.: 32 AF XY: 0.154 AC XY: 11445 AN XY: 74396

Gnomad4 AFR AF: 0.0872

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.354

Gnomad4 SAS AF: 0.199

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.151

Alfa AF: 0.153 Hom.: 946

Bravo AF: 0.140

Asia WGS AF: 0.252 AC: 876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs947699; hg19: chr10-43493897;