rs460053

Variant names:

• chr5-34971285-A-G
• rs460053

Your query was ambiguous. Multiple possible variants found:

• chr5-34971285-A-G
• chr5-34971285-A-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 0.32 in 152,050 control chromosomes in the GnomAD database, including 7,903 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 0.32 (7903 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.62).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.387 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: 0.320 AC: 48654 AN: 151932 Hom.: 7888 Cov.: 31

Gnomad AFR AF: 0.269

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.309

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.310

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

GnomAD4 genome AF: 0.320 AC: 48706 AN: 152050 Hom.: 7903 Cov.: 31 AF XY: 0.319 AC XY: 23704 AN XY: 74328

African (AFR) AF: 0.269 AC: 11178 AN: 41478

American (AMR) AF: 0.331 AC: 5062 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3472

East Asian (EAS) AF: 0.370 AC: 1907 AN: 5158

South Asian (SAS) AF: 0.401 AC: 1931 AN: 4810

European-Finnish (FIN) AF: 0.309 AC: 3267 AN: 10560

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23290 AN: 67960

Other (OTH) AF: 0.312 AC: 658 AN: 2110

Alfa AF: 0.327 Hom.: 2976

Bravo AF: 0.321

Asia WGS AF: 0.387 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.62
CADD	Benign	8.0
DANN	Benign	0.92
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs460053; hg19: chr5-34971390;