rs12870589

chr13-97572967-A-G

Variant summary

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

The XR_007063845.1(LOC105370324):n.2615-25616T>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 0.612 in 151,498 control chromosomes in the GnomAD database, including 30,648 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 0.61 (30648 hom., cov: 29)
• Consequence: LOC105370324 XR_007063845.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409

Genes affected

LOC105370324 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370324	XR_007063845.1	n.2615-25616T>C		intron_variant, non_coding_transcript_variant
LOC105370324	XR_931663.3	n.2671-25616T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.613 AC: 92728 AN: 151382 Hom.: 30642 Cov.: 29

Gnomad AFR AF: 0.349

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.700

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.719

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.662

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

GnomAD4 genome AF: 0.612 AC: 92760 AN: 151498 Hom.: 30648 Cov.: 29 AF XY: 0.617 AC XY: 45626 AN XY: 74004

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.476

Gnomad4 SAS AF: 0.705

Gnomad4 FIN AF: 0.719

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.662

Alfa AF: 0.721 Hom.: 59954

Bravo AF: 0.598

Asia WGS AF: 0.562 AC: 1956 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	14
Dann	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12870589; hg19: chr13-98225221;