rs873330

chr13-104807897-A-G

Variant summary

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

The XR_001749995.2(LOC107984606):n.296+29306T>C 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 0.312 in 152,086 control chromosomes in the GnomAD database, including 8,727 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 0.31 (8727 hom., cov: 33)
• Consequence: LOC107984606 XR_001749995.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.830

Genes affected

LOC107984606 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107984606	XR_001749995.2	n.296+29306T>C		intron_variant, non_coding_transcript_variant
LOC107984606	XR_001749993.2	n.422-2279T>C		intron_variant, non_coding_transcript_variant
LOC107984606	XR_001749994.2	n.297-2279T>C		intron_variant, non_coding_transcript_variant
LOC107984606	XR_007063859.1	n.421+15766T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47432 AN: 151968 Hom.: 8732 Cov.: 33

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.475

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.300

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

GnomAD4 genome AF: 0.312 AC: 47420 AN: 152086 Hom.: 8727 Cov.: 33 AF XY: 0.315 AC XY: 23448 AN XY: 74344

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.265

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.297

Alfa AF: 0.346 Hom.: 1324

Bravo AF: 0.292

Asia WGS AF: 0.335 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.7
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs873330; hg19: chr13-105460248;