7-72841239-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.679 AC: 28135 AN: 41456

American (AMR) AF: 0.698 AC: 10617 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2638 AN: 3468

East Asian (EAS) AF: 0.450 AC: 2325 AN: 5166

South Asian (SAS) AF: 0.743 AC: 3576 AN: 4816

European-Finnish (FIN) AF: 0.771 AC: 8152 AN: 10578

Middle Eastern (MID) AF: 0.760 AC: 222 AN: 292

European-Non Finnish (NFE) AF: 0.788 AC: 53589 AN: 67982

Other (OTH) AF: 0.734 AC: 1546 AN: 2106

Alfa AF: 0.754 Hom.: 37072

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
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2058059; hg19: chr7-72311817;