rs2391778

Positions:

• chr13-109606206-T-A
• chr13-109606206-T-C

Variant summary

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

The XR_007063870.1(LOC124903210):​n.940+3A>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 152,078 control chromosomes in the GnomAD database, including 20,304 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 0.51 (20304 hom., cov: 33)
• Consequence: LOC124903210 XR_007063870.1 splice_region, intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0250

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.940+3A>T		splice_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285534	ENST00000650264.1	n.759-35048A>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76929 AN: 151960 Hom.: 20268 Cov.: 33

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.314

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.611

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.506 AC: 77017 AN: 152078 Hom.: 20304 Cov.: 33 AF XY: 0.510 AC XY: 37937 AN XY: 74332

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.540

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.495

Alfa AF: 0.473 Hom.: 2166

Bravo AF: 0.519

Asia WGS AF: 0.566 AC: 1968 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.30
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2391778; hg19: chr13-110258553;