rs858535

Variant names:

• chr1-167522248-A-C
• rs858535

Your query was ambiguous. Multiple possible variants found:

• chr1-167522248-A-C
• chr1-167522248-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 0.364 in 152,098 control chromosomes in the GnomAD database, including 11,690 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 (11690 hom., cov: 32)
• Consequence: AKR1D1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 4 publications found

Genes affected

AKR1D1P1 (HGNC:11288): (aldo-keto reductase family 1 member D1 pseudogene 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.495 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: 0.364 AC: 55368 AN: 151980 Hom.: 11684 Cov.: 32

Gnomad AFR AF: 0.174

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0779

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.321

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.364 AC: 55395 AN: 152098 Hom.: 11690 Cov.: 32 AF XY: 0.365 AC XY: 27123 AN XY: 74316

African (AFR) AF: 0.174 AC: 7205 AN: 41514

American (AMR) AF: 0.504 AC: 7705 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1195 AN: 3472

East Asian (EAS) AF: 0.0779 AC: 404 AN: 5186

South Asian (SAS) AF: 0.415 AC: 1998 AN: 4814

European-Finnish (FIN) AF: 0.442 AC: 4662 AN: 10552

Middle Eastern (MID) AF: 0.331 AC: 96 AN: 290

European-Non Finnish (NFE) AF: 0.457 AC: 31072 AN: 67964

Other (OTH) AF: 0.379 AC: 799 AN: 2106

Alfa AF: 0.379 Hom.: 2882

Bravo AF: 0.357

Asia WGS AF: 0.292 AC: 1015 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	5.1
DANN	Benign	0.64
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs858535; hg19: chr1-167491485;