rs951095

Positions:

• chr13-104826293-C-T

Variant summary

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

The XR_001749995.2(LOC107984606):​n.296+10910G>A 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 0.384 in 151,906 control chromosomes in the GnomAD database, including 11,588 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 0.38 (11588 hom., cov: 31)
• Consequence: LOC107984606 XR_001749995.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

Genes affected

LOC107984606 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107984606	XR_001749995.2	n.296+10910G>A		intron_variant, non_coding_transcript_variant
LOC107984607	XR_007063861.1	n.87+2814C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58374 AN: 151788 Hom.: 11591 Cov.: 31

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.247

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.343

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

GnomAD4 genome AF: 0.384 AC: 58393 AN: 151906 Hom.: 11588 Cov.: 31 AF XY: 0.397 AC XY: 29462 AN XY: 74204

Gnomad4 AFR AF: 0.385

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.247

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.340

Alfa AF: 0.347 Hom.: 19759

Bravo AF: 0.379

Asia WGS AF: 0.415 AC: 1445 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951095; hg19: chr13-105478644;