chr10-30378681-A-T

Variant names:

• chr10-30378681-A-T
• rs1963187

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 0.932 in 152,320 control chromosomes in the GnomAD database, including 66,212 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 0.93 (66212 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.937 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: 0.932 AC: 141864 AN: 152202 Hom.: 66165 Cov.: 33

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.953

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.929

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.966

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.943

Gnomad OTH AF: 0.923

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

GnomAD4 genome AF: 0.932 AC: 141968 AN: 152320 Hom.: 66212 Cov.: 33 AF XY: 0.931 AC XY: 69364 AN XY: 74486

Gnomad4 AFR AF: 0.914

Gnomad4 AMR AF: 0.934

Gnomad4 ASJ AF: 0.895

Gnomad4 EAS AF: 0.929

Gnomad4 SAS AF: 0.888

Gnomad4 FIN AF: 0.966

Gnomad4 NFE AF: 0.943

Gnomad4 OTH AF: 0.922

Alfa AF: 0.936 Hom.: 8274

Bravo AF: 0.930

Asia WGS AF: 0.896 AC: 3114 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	9.9
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1963187; hg19: chr10-30667610;