1-240007496-T-C

Position:

• chr1-240007496-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The 1-240007496-T-C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 151,778 control chromosomes in the GnomAD database, including 11,754 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 0.39 (11754 hom., cov: 31)
• Consequence: RPS7P5 NR_036695.2 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RPS7P5	NR_036695.2			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000668221.1			upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58736 AN: 151660 Hom.: 11755 Cov.: 31

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.387 AC: 58746 AN: 151778 Hom.: 11754 Cov.: 31 AF XY: 0.385 AC XY: 28577 AN XY: 74152

Gnomad4 AFR AF: 0.338

Gnomad4 AMR AF: 0.318

Gnomad4 ASJ AF: 0.483

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.410

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.390

Alfa AF: 0.420 Hom.: 18738

Bravo AF: 0.375

Asia WGS AF: 0.277 AC: 967 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2065914; hg19: chr1-240170796;