rs7530595

Positions:

• chr1-23954616-C-T

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 0.318 in 151,876 control chromosomes in the GnomAD database, including 9,286 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 0.32 (9286 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.945

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.23954616C>T		intergenic_region
LOC124903877	XR_007065541.1	n.17-1540G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.318 AC: 48264 AN: 151758 Hom.: 9278 Cov.: 31

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.287

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.318 AC: 48282 AN: 151876 Hom.: 9286 Cov.: 31 AF XY: 0.316 AC XY: 23431 AN XY: 74212

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.357

Gnomad4 SAS AF: 0.251

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.325

Alfa AF: 0.391 Hom.: 9507

Bravo AF: 0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.9
DANN	Benign	0.92

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7530595; hg19: chr1-24281106;