13-31442296-A-G

Position:

• chr13-31442296-A-G

Variant summary

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

The XR_941830.1(LOC105370150):​n.234-1069A>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 0.366 in 152,052 control chromosomes in the GnomAD database, including 10,547 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 0.37 (10547 hom., cov: 32)
• Consequence: LOC105370150 XR_941830.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68

Genes affected

LOC105370150 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370150	XR_941830.1	n.234-1069A>G		intron_variant, non_coding_transcript_variant
LOC105370150	XR_001749806.1	n.360-1069A>G		intron_variant, non_coding_transcript_variant
LOC105370150	XR_941829.1	n.232-1069A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55478 AN: 151932 Hom.: 10505 Cov.: 32

Gnomad AFR AF: 0.465

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.302

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.366 AC: 55580 AN: 152052 Hom.: 10547 Cov.: 32 AF XY: 0.368 AC XY: 27369 AN XY: 74322

Gnomad4 AFR AF: 0.466

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.302

Gnomad4 SAS AF: 0.368

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.342

Alfa AF: 0.325 Hom.: 3862

Bravo AF: 0.370

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	15
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1328949; hg19: chr13-32016433;