7-145031198-C-T

Variant names:

• chr7-145031198-C-T
• rs1525461

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 0.729 in 152,104 control chromosomes in the GnomAD database, including 41,425 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 0.73 (41425 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 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: 0.729 AC: 110828 AN: 151986 Hom.: 41419 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.832

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.724

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.737

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

GnomAD4 genome AF: 0.729 AC: 110867 AN: 152104 Hom.: 41425 Cov.: 32 AF XY: 0.730 AC XY: 54269 AN XY: 74354

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.671

Gnomad4 ASJ AF: 0.724

Gnomad4 EAS AF: 0.842

Gnomad4 SAS AF: 0.700

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.739

Alfa AF: 0.774 Hom.: 22887

Bravo AF: 0.708

Asia WGS AF: 0.749 AC: 2604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.0
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1525461; hg19: chr7-144728291;