13-109590670-G-C

Position:

• chr13-109590670-G-C

Variant summary

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

The XR_007063870.1(LOC124903210):​n.2619C>G 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 0.302 in 151,962 control chromosomes in the GnomAD database, including 7,342 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 0.30 (7342 hom., cov: 32)
• Consequence: LOC124903210 XR_007063870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900

Genes affected

LOC124903210 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903210	XR_007063870.1	n.2619C>G		non_coding_transcript_exon_variant	2/2
LOC101927627	XR_007063867.1	n.77+152G>C		intron_variant, non_coding_transcript_variant
LOC101927627	XR_007063868.1	n.64+152G>C		intron_variant, non_coding_transcript_variant
LOC101927627	XR_007063869.1	n.77+152G>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650264.1	n.759-19512C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.302 AC: 45880 AN: 151844 Hom.: 7334 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.533

Gnomad SAS AF: 0.504

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.323

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.302 AC: 45901 AN: 151962 Hom.: 7342 Cov.: 32 AF XY: 0.304 AC XY: 22565 AN XY: 74278

Gnomad4 AFR AF: 0.245

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.323

Gnomad4 OTH AF: 0.298

Alfa AF: 0.195 Hom.: 469

Bravo AF: 0.295

Asia WGS AF: 0.463 AC: 1609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.67
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs914270; hg19: chr13-110243017;