rs214209

Variant names:

• chr1-48119411-C-A
• rs214209
• ENST00000452503.1:n.409+8497G>T

Your query was ambiguous. Multiple possible variants found:

• chr1-48119411-C-A
• chr1-48119411-C-G
• chr1-48119411-C-T

Variant summary

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

The ENST00000452503.1(ENSG00000290466):​n.409+8497G>T 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: 31)
• Consequence: ENSG00000290466 ENST00000452503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 2 publications found

Genes affected

ENSG00000290466 (HGNC:):

SKINT1L (HGNC:33993): (Skint1 like (pseudogene))

LINC02794 (HGNC:54318): (long intergenic non-protein coding RNA 2794)

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=-0.94).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SKINT1L	NR_026749.2	n.1275+8497G>T		intron_variant	Intron 9 of 9
LINC02794	XR_007066068.1	n.3463+18559C>A		intron_variant	Intron 8 of 12
LINC02794	XR_007066069.1	n.3463+18559C>A		intron_variant	Intron 8 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290466	ENST00000452503.1	n.409+8497G>T		intron_variant	Intron 4 of 4	2
ENSG00000290466	ENST00000604015.1	n.41+8497G>T		intron_variant	Intron 1 of 1	4
ENSG00000290466	ENST00000706231.2	n.1048-17461G>T		intron_variant	Intron 7 of 7
ENSG00000290466	ENST00000788051.1	n.720+8497G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.057
DANN	Benign	0.61
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs214209; hg19: chr1-48585083;