10-130783070-C-T

Variant names:

• chr10-130783070-C-T
• rs1911999

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 0.505 in 152,036 control chromosomes in the GnomAD database, including 23,525 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 0.50 (23525 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.713 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: 0.505 AC: 76752 AN: 151918 Hom.: 23531 Cov.: 33

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.781

Gnomad AMR AF: 0.612

Gnomad ASJ AF: 0.655

Gnomad EAS AF: 0.732

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.602

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.505 AC: 76735 AN: 152036 Hom.: 23525 Cov.: 33 AF XY: 0.509 AC XY: 37813 AN XY: 74290

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.655

Gnomad4 EAS AF: 0.732

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.519

Alfa AF: 0.621 Hom.: 33901

Bravo AF: 0.486

Asia WGS AF: 0.547 AC: 1901 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1911999; hg19: chr10-132581334;