rs7456425

Variant names:

• chr7-81835392-C-T
• rs7456425

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.0694 AC: 2879 AN: 41496

American (AMR) AF: 0.112 AC: 1706 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3466

East Asian (EAS) AF: 0.0580 AC: 300 AN: 5168

South Asian (SAS) AF: 0.140 AC: 673 AN: 4816

European-Finnish (FIN) AF: 0.172 AC: 1811 AN: 10536

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12932 AN: 67934

Other (OTH) AF: 0.137 AC: 289 AN: 2106

Alfa AF: 0.182 Hom.: 1704

Bravo AF: 0.136

Asia WGS AF: 0.0940 AC: 331 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.5
DANN	Benign	0.48
PhyloP100		0.0030

Splicing

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

Other links and lift over

dbSNP: rs7456425; hg19: chr7-81464708;