rs1538142

Positions:

• chr13-37872295-C-T

Variant summary

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

The ENST00000660705.1(ENSG00000287477):​n.933C>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: ENST00000660705.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC124903160	XR_007063762.1	n.1615C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000660705.1	n.933C>T		non_coding_transcript_exon_variant	2/2

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

Gnomad4 AFR AF: 0.0689

Gnomad4 AMR AF: 0.0250

Gnomad4 ASJ AF: 0.0597

Gnomad4 EAS AF: 0.0145

Gnomad4 SAS AF: 0.0413

Gnomad4 FIN AF: 0.0149

Gnomad4 NFE AF: 0.0271

Gnomad4 OTH AF: 0.0412

Alfa AF: 0.0336 Hom.: 13

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1538142; hg19: chr13-38446432;