rs13378957

Positions:

• chr13-20323793-A-C
• chr13-20323793-A-G
• chr13-20323793-A-T

Variant summary

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

The XR_941720.2(LOC105370102):​n.201-1572A>C 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 0.193 in 152,138 control chromosomes in the GnomAD database, including 3,565 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 0.19 (3565 hom., cov: 31)
• Consequence: LOC105370102 XR_941720.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.887

Genes affected

LOC105370102 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370102	XR_941720.2	n.201-1572A>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29350 AN: 152020 Hom.: 3574 Cov.: 31

Gnomad AFR AF: 0.0553

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.321

Gnomad EAS AF: 0.424

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.263

Gnomad MID AF: 0.252

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.193 AC: 29330 AN: 152138 Hom.: 3565 Cov.: 31 AF XY: 0.201 AC XY: 14947 AN XY: 74380

Gnomad4 AFR AF: 0.0552

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.321

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.315

Gnomad4 FIN AF: 0.263

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.202

Alfa AF: 0.107 Hom.: 171

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13378957; hg19: chr13-20897932;