rs1454520

Variant names:

• chr7-54613210-G-A
• rs1454520

Your query was ambiguous. Multiple possible variants found:

• chr7-54613210-G-A
• chr7-54613210-G-C

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 0.379 in 151,826 control chromosomes in the GnomAD database, including 12,400 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 0.38 (12400 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.379 AC: 57555 AN: 151710 Hom.: 12402 Cov.: 33

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.544

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.379 AC: 57555 AN: 151826 Hom.: 12400 Cov.: 33 AF XY: 0.395 AC XY: 29333 AN XY: 74240

African (AFR) AF: 0.195 AC: 8070 AN: 41424

American (AMR) AF: 0.469 AC: 7157 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1409 AN: 3462

East Asian (EAS) AF: 0.739 AC: 3828 AN: 5178

South Asian (SAS) AF: 0.591 AC: 2849 AN: 4822

European-Finnish (FIN) AF: 0.544 AC: 5711 AN: 10496

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27327 AN: 67868

Other (OTH) AF: 0.381 AC: 804 AN: 2112

Alfa AF: 0.398 Hom.: 7224

Bravo AF: 0.363

Asia WGS AF: 0.597 AC: 2061 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.1
DANN	Benign	0.76
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs1454520; hg19: chr7-54680903;