rs1581675

Variant names:

• chr8-20000988-T-A
• rs1581675

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.233 in 152,068 control chromosomes in the GnomAD database, including 4,311 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 0.23 (4311 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.267 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: 0.233 AC: 35478 AN: 151950 Hom.: 4312 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.232

Gnomad ASJ AF: 0.338

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.270

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.233 AC: 35470 AN: 152068 Hom.: 4311 Cov.: 32 AF XY: 0.233 AC XY: 17293 AN XY: 74320

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.232

Gnomad4 ASJ AF: 0.338

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.230

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.270

Gnomad4 OTH AF: 0.237

Alfa AF: 0.247 Hom.: 579

Bravo AF: 0.228

Asia WGS AF: 0.233 AC: 810 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	3.9
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1581675; hg19: chr8-19858499;