rs7530810

Variant names:

• chr1-115027847-G-A
• rs7530810

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 0.398 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.205 AC: 8491 AN: 41402

American (AMR) AF: 0.395 AC: 6018 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.539 AC: 1870 AN: 3468

East Asian (EAS) AF: 0.498 AC: 2574 AN: 5172

South Asian (SAS) AF: 0.385 AC: 1856 AN: 4816

European-Finnish (FIN) AF: 0.400 AC: 4201 AN: 10504

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.500 AC: 33942 AN: 67920

Other (OTH) AF: 0.428 AC: 900 AN: 2102

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
PhyloP100		0.98

Splicing

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

Other links and lift over

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