13-37489219-C-T

Variant summary

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

The XR_007063761.1(LOC124903159):n.343-1208C>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 0.0791 in 152,070 control chromosomes in the GnomAD database, including 1,148 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 0.079 (1148 hom., cov: 32)
• Consequence: LOC124903159 XR_007063761.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

Genes affected

LOC124903159 (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 = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903159	XR_007063761.1	n.343-1208C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0789 AC: 11991 AN: 151952 Hom.: 1143 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0410

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.00594

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0160

Gnomad OTH AF: 0.0728

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

GnomAD4 genome AF: 0.0791 AC: 12022 AN: 152070 Hom.: 1148 Cov.: 32 AF XY: 0.0801 AC XY: 5956 AN XY: 74332

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.0409

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.000966

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.00594

Gnomad4 NFE AF: 0.0160

Gnomad4 OTH AF: 0.0716

Alfa AF: 0.0148 Hom.: 18

Bravo AF: 0.0858

Asia WGS AF: 0.0620 AC: 215 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	6.2
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17055889; hg19: chr13-38063356;