13-21811591-T-C

Position:

• chr13-21811591-T-C

Variant summary

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

The XR_007063714.1(LOC124903132):​n.216-1967T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.589 in 145,790 control chromosomes in the GnomAD database, including 25,681 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 0.59 (25681 hom., cov: 22)
• Consequence: LOC124903132 XR_007063714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.333

Genes affected

LOC124903132 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.654 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903132	XR_007063714.1	n.216-1967T>C		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.589 AC: 85773 AN: 145676 Hom.: 25665 Cov.: 22

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.718

Gnomad MID AF: 0.569

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.589 AC: 85831 AN: 145790 Hom.: 25681 Cov.: 22 AF XY: 0.585 AC XY: 41435 AN XY: 70870

Gnomad4 AFR AF: 0.507

Gnomad4 AMR AF: 0.551

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.718

Gnomad4 NFE AF: 0.660

Gnomad4 OTH AF: 0.601

Alfa AF: 0.628 Hom.: 27151

Bravo AF: 0.556

Asia WGS AF: 0.358 AC: 1244 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.11
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: rs9316567; hg19: chr13-22385730;