7-72841239-C-T

Variant names:

• chr7-72841239-C-T
• rs2058059
• ENST00000488637.3:n.*198G>A

Variant summary

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

The ENST00000488637.3(RN7SL625P):​n.*198G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 151,982 control chromosomes in the GnomAD database, including 41,417 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 0.73 (41417 hom., cov: 30)
• Consequence: RN7SL625P ENST00000488637.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

Genes affected

RN7SL625P (HGNC:46641): (RNA, 7SL, cytoplasmic 625, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.783 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
RN7SL625P	ENST00000488637.3	n.*198G>A		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111497 AN: 151864 Hom.: 41400 Cov.: 30

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.835

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.752

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.734 AC: 111560 AN: 151982 Hom.: 41417 Cov.: 30 AF XY: 0.730 AC XY: 54235 AN XY: 74260

Gnomad4 AFR AF: 0.679

Gnomad4 AMR AF: 0.698

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.743

Gnomad4 FIN AF: 0.771

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.734

Alfa AF: 0.778 Hom.: 14619

Bravo AF: 0.722

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.6

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2058059; hg19: chr7-72311817;