1-48164766-G-C

Position:

• chr1-48164766-G-C

Variant summary

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

The NR_026749.2(SKINT1L):​n.693C>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 NR_026749.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SKINT1L	NR_026749.2	n.693C>G		non_coding_transcript_exon_variant	5/10
LINC02794	XR_007066068.1	n.3673+5340G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SKINT1L	ENST00000401057.7	n.571C>G		non_coding_transcript_exon_variant	3/4
	ENST00000706231.1	n.693C>G		non_coding_transcript_exon_variant	5/5

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

Gnomad4 ASJ exome AF: 1.00

Gnomad4 NFE exome AF: 0.625

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

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.561

Gnomad4 ASJ AF: 0.777

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.672

Gnomad4 OTH AF: 0.665

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10788882; hg19: chr1-48630438;