rs816958

chr13-107870547-A-Gchr13-107870547-A-T

Variant summary

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

The XM_047430833.1(LOC124903206):c.*3087A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,108 control chromosomes in the GnomAD database, including 26,333 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 0.58 (26332 hom., cov: 33)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LOC124903206 XM_047430833.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0140

Genes affected

LOC124903206 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124903206	XM_047430833.1	c.*3087A>G		3_prime_UTR_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000622038.1	n.165A>G		non_coding_transcript_exon_variant	1/1
	ENST00000663056.1	n.104+1621A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.578 AC: 87861 AN: 151988 Hom.: 26271 Cov.: 33

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.420

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.624

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.486

Gnomad OTH AF: 0.576

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.578 AC: 87991 AN: 152106 Hom.: 26332 Cov.: 33 AF XY: 0.584 AC XY: 43436 AN XY: 74360

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.788

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.486

Gnomad4 OTH AF: 0.578

Alfa AF: 0.509 Hom.: 22354

Bravo AF: 0.587

Asia WGS AF: 0.696 AC: 2419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	4.1
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs816958; hg19: chr13-108522895;