rs1015213

chr8-51974981-C-T

Variant summary

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

The ENST00000521188.1(ENSG00000253844):n.113+13411C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,086 control chromosomes in the GnomAD database, including 2,200 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 0.14 (2200 hom., cov: 32)
• Consequence: ENST00000521188.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901944	XR_007060910.1	n.115+1246C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000521188.1	n.113+13411C>T		intron_variant, non_coding_transcript_variant		3
	ENST00000702548.1	n.115+1246C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20515 AN: 151968 Hom.: 2194 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0593

Gnomad AMR AF: 0.0801

Gnomad ASJ AF: 0.0816

Gnomad EAS AF: 0.0169

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.0377

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0815

Gnomad OTH AF: 0.134

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

GnomAD4 genome AF: 0.135 AC: 20552 AN: 152086 Hom.: 2200 Cov.: 32 AF XY: 0.131 AC XY: 9728 AN XY: 74360

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.0800

Gnomad4 ASJ AF: 0.0816

Gnomad4 EAS AF: 0.0176

Gnomad4 SAS AF: 0.0893

Gnomad4 FIN AF: 0.0377

Gnomad4 NFE AF: 0.0815

Gnomad4 OTH AF: 0.133

Alfa AF: 0.0911 Hom.: 1240

Bravo AF: 0.143

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.26
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1015213; hg19: chr8-52887541;