rs1524395

chr7-54130808-C-Achr7-54130808-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 0.357 in 151,992 control chromosomes in the GnomAD database, including 10,419 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 0.36 (10419 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.356 AC: 54109 AN: 151874 Hom.: 10394 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.246

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.357 AC: 54190 AN: 151992 Hom.: 10419 Cov.: 32 AF XY: 0.360 AC XY: 26736 AN XY: 74288

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.359

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.304

Alfa AF: 0.283 Hom.: 6455

Bravo AF: 0.361

Asia WGS AF: 0.316 AC: 1099 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	0.071
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1524395; hg19: chr7-54198501;