rs1041466

chr13-109591975-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.1314T>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 0.361 in 152,070 control chromosomes in the GnomAD database, including 11,370 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 0.36 (11370 hom., cov: 32)
• Consequence: LOC124903210 XR_007063870.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.603

Genes affected

LOC124903210 (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 (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903210	XR_007063870.1	n.1314T>C		non_coding_transcript_exon_variant	2/2
LOC101927627	XR_007063867.1	n.77+1457A>G		intron_variant, non_coding_transcript_variant
LOC101927627	XR_007063868.1	n.129+646A>G		intron_variant, non_coding_transcript_variant
LOC101927627	XR_007063869.1	n.77+1457A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000650264.1	n.759-20817T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.361 AC: 54832 AN: 151952 Hom.: 11360 Cov.: 32

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.0980

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.541

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.361 AC: 54869 AN: 152070 Hom.: 11370 Cov.: 32 AF XY: 0.356 AC XY: 26440 AN XY: 74372

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.0980

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.541

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.370

Alfa AF: 0.431 Hom.: 15057

Bravo AF: 0.336

Asia WGS AF: 0.183 AC: 641 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	0.15
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1041466; hg19: chr13-110244322;