rs13116912

Positions:

• chr4-110251341-A-C
• chr4-110251341-A-T

Variant summary

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

The XR_007058229.1(LOC124900759):​n.290+545A>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 0.0609 in 152,266 control chromosomes in the GnomAD database, including 593 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 0.061 (593 hom., cov: 32)
• Consequence: LOC124900759 XR_007058229.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0440

Genes affected

LOC124900759 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124900759	XR_007058229.1	n.290+545A>C		intron_variant, non_coding_transcript_variant
LOC124900759	XR_007058228.1	n.394+545A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0608 AC: 9253 AN: 152148 Hom.: 591 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0397

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.00766

Gnomad FIN AF: 0.0191

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0240

Gnomad OTH AF: 0.0511

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

GnomAD4 genome AF: 0.0609 AC: 9268 AN: 152266 Hom.: 593 Cov.: 32 AF XY: 0.0590 AC XY: 4393 AN XY: 74452

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.0396

Gnomad4 ASJ AF: 0.0550

Gnomad4 EAS AF: 0.0112

Gnomad4 SAS AF: 0.00746

Gnomad4 FIN AF: 0.0191

Gnomad4 NFE AF: 0.0240

Gnomad4 OTH AF: 0.0520

Alfa AF: 0.0294 Hom.: 83

Bravo AF: 0.0684

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.6
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13116912; hg19: chr4-111172497;