rs1343692

Positions:

• chr13-76255012-G-A
• chr13-76255012-G-T

Variant summary

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

The XR_942093.3(LOC105370262):​n.76-7082C>T 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 0.156 in 152,050 control chromosomes in the GnomAD database, including 2,020 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 0.16 (2020 hom., cov: 32)
• Consequence: LOC105370262 XR_942093.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

Genes affected

LOC105370262 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370262	XR_942093.3	n.76-7082C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23660 AN: 151932 Hom.: 2023 Cov.: 32

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.244

Gnomad EAS AF: 0.0340

Gnomad SAS AF: 0.274

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.156 AC: 23665 AN: 152050 Hom.: 2020 Cov.: 32 AF XY: 0.154 AC XY: 11455 AN XY: 74334

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.244

Gnomad4 EAS AF: 0.0341

Gnomad4 SAS AF: 0.274

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.185

Alfa AF: 0.167 Hom.: 281

Bravo AF: 0.155

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1343692; hg19: chr13-76829148;