rs1411765

chr13-109606721-A-G

Variant summary

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

The XR_007063870.1(LOC124903210):n.428T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.508 in 152,110 control chromosomes in the GnomAD database, including 20,431 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 0.51 (20431 hom., cov: 33)
• Consequence: LOC124903210 XR_007063870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.803

Genes affected

LOC124903210 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903210	XR_007063870.1	n.428T>C		non_coding_transcript_exon_variant	1/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650264.1	n.759-35563T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.508 AC: 77222 AN: 151992 Hom.: 20395 Cov.: 33

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.312

Gnomad AMR AF: 0.540

Gnomad ASJ AF: 0.421

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.612

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.430

Gnomad OTH AF: 0.498

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

GnomAD4 genome AF: 0.508 AC: 77310 AN: 152110 Hom.: 20431 Cov.: 33 AF XY: 0.513 AC XY: 38122 AN XY: 74354

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.421

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.613

Gnomad4 FIN AF: 0.402

Gnomad4 NFE AF: 0.430

Gnomad4 OTH AF: 0.497

Alfa AF: 0.461 Hom.: 9727

Bravo AF: 0.520

Asia WGS AF: 0.566 AC: 1969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.14
Dann	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1411765; hg19: chr13-110259068;