rs1538142

Variant names:

• chr13-37872295-C-T
• rs1538142
• ENST00000660705.2:n.1011C>T

Variant summary

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

The ENST00000660705.2(ENSG00000287477):​n.1011C>T 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 0.0391 in 152,212 control chromosomes in the GnomAD database, including 155 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 0.039 (155 hom., cov: 32)
• Consequence: ENSG00000287477 ENST00000660705.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 1 publications found

Genes affected

ENSG00000287477 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0667 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903160	XR_007063762.1	n.1615C>T		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287477	ENST00000660705.2	n.1011C>T		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000309047	ENST00000838014.1	n.262G>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000309047	ENST00000838015.1	n.161G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0390 AC: 5932 AN: 152094 Hom.: 153 Cov.: 32

Gnomad AFR AF: 0.0688

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0250

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.0142

Gnomad SAS AF: 0.0404

Gnomad FIN AF: 0.0149

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0271

Gnomad OTH AF: 0.0416

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

GnomAD4 genome AF: 0.0391 AC: 5946 AN: 152212 Hom.: 155 Cov.: 32 AF XY: 0.0388 AC XY: 2888 AN XY: 74408

African (AFR) AF: 0.0689 AC: 2858 AN: 41508

American (AMR) AF: 0.0250 AC: 382 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3470

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5188

South Asian (SAS) AF: 0.0413 AC: 199 AN: 4824

European-Finnish (FIN) AF: 0.0149 AC: 158 AN: 10602

Middle Eastern (MID) AF: 0.0646 AC: 19 AN: 294

European-Non Finnish (NFE) AF: 0.0271 AC: 1842 AN: 68008

Other (OTH) AF: 0.0412 AC: 87 AN: 2112

Alfa AF: 0.0355 Hom.: 15

Bravo AF: 0.0416

Asia WGS AF: 0.0260 AC: 89 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.048
DANN	Benign	0.48
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1538142; hg19: chr13-38446432;