rs589636

chr13-76942441-T-C

Variant summary

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

The XR_001749929.1(LOC105370269):n.323+320A>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 0.815 in 152,154 control chromosomes in the GnomAD database, including 50,807 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 0.82 (50807 hom., cov: 32)
• Consequence: LOC105370269 XR_001749929.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.67

Genes affected

LOC105370269 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370269	XR_001749929.1	n.323+320A>G		intron_variant, non_coding_transcript_variant
LOC105370269	XR_942104.2	n.200+320A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123962 AN: 152038 Hom.: 50782 Cov.: 32

Gnomad AFR AF: 0.798

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.890

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.551

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.886

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.825

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

GnomAD4 genome AF: 0.815 AC: 124040 AN: 152154 Hom.: 50807 Cov.: 32 AF XY: 0.809 AC XY: 60180 AN XY: 74378

Gnomad4 AFR AF: 0.798

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.890

Gnomad4 EAS AF: 0.759

Gnomad4 SAS AF: 0.551

Gnomad4 FIN AF: 0.788

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.824

Alfa AF: 0.833 Hom.: 13094

Bravo AF: 0.825

Asia WGS AF: 0.663 AC: 2308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.40
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs589636; hg19: chr13-77516576;