13-109590670-G-C

Variant names:

• chr13-109590670-G-C
• rs914270
• XR_007063870.1:n.2619C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC124903210 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.2619C>G		non_coding_transcript_exon_variant	Exon 2 of 2
LOC101927627	XR_007063867.1	n.77+152G>C		intron_variant	Intron 1 of 3
LOC101927627	XR_007063868.1	n.64+152G>C		intron_variant	Intron 1 of 4
LOC101927627	XR_007063869.1	n.77+152G>C		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285534	ENST00000650264.1	n.759-19512C>G		intron_variant	Intron 1 of 3
ENSG00000296995	ENST00000744136.1	n.227+152G>C		intron_variant	Intron 1 of 4
ENSG00000296995	ENST00000744137.1	n.222+152G>C		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.245 AC: 10156 AN: 41444

American (AMR) AF: 0.268 AC: 4086 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1043 AN: 3464

East Asian (EAS) AF: 0.534 AC: 2738 AN: 5130

South Asian (SAS) AF: 0.505 AC: 2429 AN: 4812

European-Finnish (FIN) AF: 0.250 AC: 2641 AN: 10560

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.323 AC: 21968 AN: 67968

Other (OTH) AF: 0.298 AC: 630 AN: 2114

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
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs914270; hg19: chr13-110243017;