rs7456425

chr7-81835392-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 0.144 in 151,990 control chromosomes in the GnomAD database, including 1,941 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 0.14 (1941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

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 (NFE) allele frequency at 95% confidence interval = 0.188 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: 0.145 AC: 21963 AN: 151872 Hom.: 1943 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0577

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.144 AC: 21962 AN: 151990 Hom.: 1941 Cov.: 32 AF XY: 0.142 AC XY: 10538 AN XY: 74270

Gnomad4 AFR AF: 0.0694

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0580

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.190

Gnomad4 OTH AF: 0.137

Alfa AF: 0.182 Hom.: 1526

Bravo AF: 0.136

Asia WGS AF: 0.0940 AC: 331 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	2.5
Dann	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7456425; hg19: chr7-81464708;