chr13-37476314-C-T

Position:

• chr13-37476314-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.244-2291C>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 0.415 in 151,968 control chromosomes in the GnomAD database, including 15,048 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 0.42 (15048 hom., cov: 33)
• Consequence: LOC124903159 XR_007063761.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.498

Genes affected

LOC124903159 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903159	XR_007063761.1	n.244-2291C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62989 AN: 151850 Hom.: 15015 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.415 AC: 63075 AN: 151968 Hom.: 15048 Cov.: 33 AF XY: 0.417 AC XY: 31003 AN XY: 74304

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.427

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.498

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.286

Gnomad4 OTH AF: 0.407

Alfa AF: 0.348 Hom.: 1267

Bravo AF: 0.436

Asia WGS AF: 0.545 AC: 1895 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7323534; hg19: chr13-38050451; COSMIC: COSV69347236;