rs7530810

Variant names:

• chr1-115027847-G-A
• rs7530810

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 0.398 in 151,842 control chromosomes in the GnomAD database, including 13,339 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 0.40 (13339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.979

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 (NFE) allele frequency at 95% confidence interval = 0.495 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: 0.398 AC: 60407 AN: 151724 Hom.: 13341 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.468

Gnomad AMR AF: 0.394

Gnomad ASJ AF: 0.539

Gnomad EAS AF: 0.498

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.471

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.398 AC: 60415 AN: 151842 Hom.: 13339 Cov.: 32 AF XY: 0.394 AC XY: 29247 AN XY: 74180

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.539

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.428

Alfa AF: 0.445 Hom.: 2033

Bravo AF: 0.392

Asia WGS AF: 0.402 AC: 1397 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	4.7
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7530810; hg19: chr1-115570468; COSMIC: COSV56655002;