rs10040679

Variant names:

• chr5-134517641-T-C
• rs10040679
• ENST00000464317.3:n.-169T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000464317.3(RN7SL541P):​n.-169T>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,254 control chromosomes in the GnomAD database, including 1,249 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 0.12 (1249 hom., cov: 32)
• Consequence: RN7SL541P ENST00000464317.3 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108
• Publications: 4 publications found

Genes affected

RN7SL541P (HGNC:46557): (RNA, 7SL, cytoplasmic 541, pseudogene)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000464317.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RN7SL541P	ENST00000464317.3	TSL:6	n.-169T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18984 AN: 152136 Hom.: 1251 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0662

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.125 AC: 18999 AN: 152254 Hom.: 1249 Cov.: 32 AF XY: 0.122 AC XY: 9088 AN XY: 74434

African (AFR) AF: 0.111 AC: 4596 AN: 41540

American (AMR) AF: 0.113 AC: 1735 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3470

East Asian (EAS) AF: 0.165 AC: 854 AN: 5182

South Asian (SAS) AF: 0.136 AC: 655 AN: 4822

European-Finnish (FIN) AF: 0.0662 AC: 703 AN: 10620

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9513 AN: 68010

Other (OTH) AF: 0.143 AC: 301 AN: 2112

Alfa AF: 0.133 Hom.: 1858

Bravo AF: 0.126

Asia WGS AF: 0.112 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.74
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs10040679; hg19: chr5-133853332;