rs1402024

Variant names:

• chr5-160001840-T-C
• rs1402024

Your query was ambiguous. Multiple possible variants found:

• chr5-160001840-T-C
• chr5-160001840-T-G

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 0.0438 in 151,780 control chromosomes in the GnomAD database, including 203 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 0.044 (203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.32
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.0437 AC: 6623 AN: 151664 Hom.: 198 Cov.: 32

Gnomad AFR AF: 0.0314

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0530

Gnomad ASJ AF: 0.0393

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.0164

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0419

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0438 AC: 6643 AN: 151780 Hom.: 203 Cov.: 32 AF XY: 0.0432 AC XY: 3204 AN XY: 74142

African (AFR) AF: 0.0314 AC: 1299 AN: 41380

American (AMR) AF: 0.0532 AC: 811 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.0393 AC: 136 AN: 3464

East Asian (EAS) AF: 0.158 AC: 814 AN: 5168

South Asian (SAS) AF: 0.0895 AC: 431 AN: 4814

European-Finnish (FIN) AF: 0.0164 AC: 172 AN: 10490

Middle Eastern (MID) AF: 0.0753 AC: 22 AN: 292

European-Non Finnish (NFE) AF: 0.0419 AC: 2846 AN: 67920

Other (OTH) AF: 0.0502 AC: 106 AN: 2110

Alfa AF: 0.0459 Hom.: 78

Bravo AF: 0.0444

Asia WGS AF: 0.118 AC: 412 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.014
DANN	Benign	0.51
PhyloP100		-4.3

Splicing

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

Other links and lift over

dbSNP: rs1402024; hg19: chr5-159428847;