1-48164766-G-C

Variant names:

• chr1-48164766-G-C
• rs10788882
• ENST00000401057.7:n.571C>G

Variant summary

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

The ENST00000401057.7(SKINT1L):​n.571C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 152,070 control chromosomes in the GnomAD database, including 34,355 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 0.67 (34351 hom., cov: 31)
  • Exomes 𝑓: 0.67 (4 hom.)
• Consequence: SKINT1L ENST00000401057.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68
• Publications: 6 publications found

Genes affected

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

ENSG00000290466 (HGNC:):

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

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 (AFR) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SKINT1L	NR_026749.2	n.693C>G		non_coding_transcript_exon_variant	Exon 5 of 10
LINC02794	XR_007066068.1	n.3673+5340G>C		intron_variant	Intron 10 of 12
LINC02794	XR_007066070.1	n.3673+5340G>C		intron_variant	Intron 10 of 10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SKINT1L	ENST00000401057.7	n.571C>G		non_coding_transcript_exon_variant	Exon 3 of 4	6
ENSG00000290466	ENST00000706231.2	n.693C>G		non_coding_transcript_exon_variant	Exon 5 of 8
ENSG00000290466	ENST00000788051.1	n.252C>G		non_coding_transcript_exon_variant	Exon 1 of 5

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101672 AN: 151934 Hom.: 34323 Cov.: 31

Gnomad AFR AF: 0.710

Gnomad AMI AF: 0.662

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.777

Gnomad EAS AF: 0.586

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.669

GnomAD4 exome AF: 0.667 AC: 12 AN: 18 Hom.: 4 Cov.: 0 AF XY: 0.667 AC XY: 12 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.625 AC: 10 AN: 16

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.669 AC: 101740 AN: 152052 Hom.: 34351 Cov.: 31 AF XY: 0.668 AC XY: 49620 AN XY: 74320

African (AFR) AF: 0.710 AC: 29459 AN: 41476

American (AMR) AF: 0.561 AC: 8566 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.777 AC: 2695 AN: 3470

East Asian (EAS) AF: 0.586 AC: 3026 AN: 5160

South Asian (SAS) AF: 0.652 AC: 3140 AN: 4816

European-Finnish (FIN) AF: 0.658 AC: 6964 AN: 10588

Middle Eastern (MID) AF: 0.752 AC: 221 AN: 294

European-Non Finnish (NFE) AF: 0.672 AC: 45657 AN: 67962

Other (OTH) AF: 0.665 AC: 1408 AN: 2116

Alfa AF: 0.660 Hom.: 16643

Bravo AF: 0.664

Asia WGS AF: 0.623 AC: 2167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.050
DANN	Benign	0.52
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs10788882; hg19: chr1-48630438;