rs748144

chr13-112447570-A-G

Variant summary

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

The XR_944294.2(LOC105370372):n.329+27564T>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 0.637 in 152,186 control chromosomes in the GnomAD database, including 35,015 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 0.64 (35015 hom., cov: 33)
• Consequence: LOC105370372 XR_944294.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.56

Genes affected

LOC105370372 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370372	XR_944294.2	n.329+27564T>C		intron_variant, non_coding_transcript_variant
LOC105370372	XR_001750036.1	n.384+27564T>C		intron_variant, non_coding_transcript_variant
LOC105370372	XR_944292.2	n.332+27564T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.637 AC: 96892 AN: 152068 Hom.: 35020 Cov.: 33

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.752

Gnomad EAS AF: 0.366

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.651

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

GnomAD4 genome AF: 0.637 AC: 96906 AN: 152186 Hom.: 35015 Cov.: 33 AF XY: 0.636 AC XY: 47316 AN XY: 74390

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.684

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.647

Alfa AF: 0.755 Hom.: 9032

Bravo AF: 0.615

Asia WGS AF: 0.527 AC: 1836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.1
Dann	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs748144; hg19: chr13-113101884;