2-168451721-T-G

Variant names:

• chr2-168451721-T-G
• rs1453405
• ENST00000779316.1:n.154+4787A>C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000779316.1(ENSG00000301499):​n.154+4787A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: ENSG00000301499 ENST00000779316.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 5 publications found

Genes affected

ENSG00000301499 (HGNC:):

RN7SL813P (HGNC:46829): (RNA, 7SL, cytoplasmic 813, pseudogene)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724081	XR_002959433.2	n.25091+5310A>C		intron_variant	Intron 1 of 3
LOC102724081	XR_007087285.1	n.25091+5310A>C		intron_variant	Intron 1 of 3
LOC102724081	XR_007087286.1	n.25091+5310A>C		intron_variant	Intron 1 of 3
LOC102724081	XR_923566.3	n.25091+5310A>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301499	ENST00000779316.1	n.154+4787A>C		intron_variant	Intron 1 of 3
ENSG00000301499	ENST00000779317.1	n.244+5310A>C		intron_variant	Intron 2 of 4
ENSG00000301499	ENST00000779318.1	n.225+5310A>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.4
DANN	Benign	0.63
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1453405; hg19: chr2-169308231;