rs1451385

chr7-25855101-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.627 in 152,130 control chromosomes in the GnomAD database, including 31,869 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 0.63 (31869 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.778

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.22).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 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: 0.628 AC: 95426 AN: 152012 Hom.: 31877 Cov.: 33

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.852

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.181

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.748

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.627 AC: 95448 AN: 152130 Hom.: 31869 Cov.: 33 AF XY: 0.623 AC XY: 46300 AN XY: 74370

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.677

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.180

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.712

Gnomad4 NFE AF: 0.748

Gnomad4 OTH AF: 0.652

Alfa AF: 0.676 Hom.: 4592

Bravo AF: 0.615

Asia WGS AF: 0.406 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.22
Cadd	Benign	19
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1451385; hg19: chr7-25894721;