rs586851

Positions:

• chr13-98092309-C-A

Variant summary

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

The XR_931670.4(LOC105370328):​n.73-25263G>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 0.709 in 152,026 control chromosomes in the GnomAD database, including 42,084 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 0.71 (42084 hom., cov: 32)
• Consequence: LOC105370328 XR_931670.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

Genes affected

LOC105370328 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.895 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370328	XR_931670.4	n.73-25263G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.709 AC: 107754 AN: 151908 Hom.: 42090 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.904

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.862

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.726

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

GnomAD4 genome AF: 0.709 AC: 107777 AN: 152026 Hom.: 42084 Cov.: 32 AF XY: 0.701 AC XY: 52130 AN XY: 74318

Gnomad4 AFR AF: 0.455

Gnomad4 AMR AF: 0.632

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.125

Gnomad4 SAS AF: 0.588

Gnomad4 FIN AF: 0.862

Gnomad4 NFE AF: 0.901

Gnomad4 OTH AF: 0.720

Alfa AF: 0.852 Hom.: 73046

Bravo AF: 0.678

Asia WGS AF: 0.379 AC: 1320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.62
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs586851; hg19: chr13-98744563;