rs261503

Positions:

• chr13-81832985-A-G
• chr13-81832985-A-T

Variant summary

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

The XR_001750061.1(LOC105370284):​n.79-9763A>G 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 0.725 in 151,950 control chromosomes in the GnomAD database, including 40,377 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 0.73 (40377 hom., cov: 30)
• Consequence: LOC105370284 XR_001750061.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502

Genes affected

LOC105370284 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370284	XR_001750061.1	n.79-9763A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110105 AN: 151832 Hom.: 40354 Cov.: 30

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.725 AC: 110178 AN: 151950 Hom.: 40377 Cov.: 30 AF XY: 0.730 AC XY: 54208 AN XY: 74270

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.753

Gnomad4 EAS AF: 0.994

Gnomad4 SAS AF: 0.857

Gnomad4 FIN AF: 0.773

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.746

Alfa AF: 0.718 Hom.: 4642

Bravo AF: 0.715

Asia WGS AF: 0.913 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs261503; hg19: chr13-82407120;