rs1023534

Positions:

• chr7-81399583-G-A

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.247

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.81399583G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;