rs1524395

Variant names:

• chr7-54130808-C-A
• rs1524395

Your query was ambiguous. Multiple possible variants found:

• chr7-54130808-C-A
• chr7-54130808-C-T

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 0.357 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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.508 AC: 21063 AN: 41446

American (AMR) AF: 0.347 AC: 5302 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 778 AN: 3466

East Asian (EAS) AF: 0.245 AC: 1264 AN: 5152

South Asian (SAS) AF: 0.302 AC: 1454 AN: 4820

European-Finnish (FIN) AF: 0.359 AC: 3785 AN: 10552

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.288 AC: 19586 AN: 67962

Other (OTH) AF: 0.304 AC: 642 AN: 2112

Alfa AF: 0.296 Hom.: 9282

Bravo AF: 0.361

Asia WGS AF: 0.316 AC: 1099 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.071
DANN	Benign	0.46
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs1524395; hg19: chr7-54198501;