rs1001990

Variant names:

• chr10-128610590-C-T
• rs1001990

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 0.279 in 152,216 control chromosomes in the GnomAD database, including 6,275 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 0.28 (6275 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.366

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.359 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: 0.279 AC: 42451 AN: 152098 Hom.: 6259 Cov.: 34

Gnomad AFR AF: 0.363

Gnomad AMI AF: 0.313

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.279 AC: 42517 AN: 152216 Hom.: 6275 Cov.: 34 AF XY: 0.278 AC XY: 20694 AN XY: 74426

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.287

Gnomad4 SAS AF: 0.285

Gnomad4 FIN AF: 0.265

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.266

Alfa AF: 0.249 Hom.: 10043

Bravo AF: 0.276

Asia WGS AF: 0.306 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.0
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1001990; hg19: chr10-130408854; COSMIC: COSV63766147;