rs1023534

Variant names:

• chr7-81399583-G-A
• rs1023534

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 0.24 in 152,160 control chromosomes in the GnomAD database, including 4,580 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 0.24 (4580 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.33 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: 0.240 AC: 36457 AN: 152042 Hom.: 4572 Cov.: 33

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.184

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.240 AC: 36500 AN: 152160 Hom.: 4580 Cov.: 33 AF XY: 0.241 AC XY: 17925 AN XY: 74380

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.311

Gnomad4 SAS AF: 0.239

Gnomad4 FIN AF: 0.184

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.278

Alfa AF: 0.241 Hom.: 544

Bravo AF: 0.250

Asia WGS AF: 0.272 AC: 944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.1
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023534; hg19: chr7-81028899;