1-59974513-G-A

Variant names:

• chr1-59974513-G-A
• rs2554297
• ENST00000583379.2:n.*244C>T

Variant summary

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

The ENST00000583379.2(RN7SL475P):​n.*244C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 151,894 control chromosomes in the GnomAD database, including 43,511 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 0.76 (43511 hom., cov: 32)
• Consequence: RN7SL475P ENST00000583379.2 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194

Genes affected

RN7SL475P (HGNC:46491): (RNA, 7SL, cytoplasmic 475, pseudogene)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 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
RN7SL475P	ENST00000583379.2	n.*244C>T		downstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114802 AN: 151776 Hom.: 43462 Cov.: 32

Gnomad AFR AF: 0.749

Gnomad AMI AF: 0.742

Gnomad AMR AF: 0.801

Gnomad ASJ AF: 0.687

Gnomad EAS AF: 0.734

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.789

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.756 AC: 114906 AN: 151894 Hom.: 43511 Cov.: 32 AF XY: 0.761 AC XY: 56481 AN XY: 74256

Gnomad4 AFR AF: 0.750

Gnomad4 AMR AF: 0.801

Gnomad4 ASJ AF: 0.687

Gnomad4 EAS AF: 0.733

Gnomad4 SAS AF: 0.837

Gnomad4 FIN AF: 0.789

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.741

Alfa AF: 0.745 Hom.: 61566

Bravo AF: 0.753

Asia WGS AF: 0.796 AC: 2768 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.76
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2554297; hg19: chr1-60440185;