XM_047430819.1:c.*254A>G

Variant names:

• chr13-33013191-T-C
• rs397703
• XM_047430819.1:c.*254A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047430819.1(LOC124903151):​c.*254A>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 0.172 in 152,172 control chromosomes in the GnomAD database, including 2,377 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 0.17 (2377 hom., cov: 32)
• Consequence: LOC124903151 XM_047430819.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800
• Publications: 7 publications found

Genes affected

LOC124903151 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.213 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000830674.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308044	ENST00000830674.1		n.854A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000308044	ENST00000830675.1		n.1017A>G		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000308044	ENST00000830677.1		n.589A>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26115 AN: 152054 Hom.: 2373 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.172 AC: 26124 AN: 152172 Hom.: 2377 Cov.: 32 AF XY: 0.173 AC XY: 12901 AN XY: 74388

African (AFR) AF: 0.104 AC: 4330 AN: 41532

American (AMR) AF: 0.219 AC: 3357 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3472

East Asian (EAS) AF: 0.138 AC: 716 AN: 5170

South Asian (SAS) AF: 0.167 AC: 805 AN: 4820

European-Finnish (FIN) AF: 0.221 AC: 2334 AN: 10564

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13463 AN: 67998

Other (OTH) AF: 0.163 AC: 344 AN: 2110

Alfa AF: 0.186 Hom.: 1284

Bravo AF: 0.170

Asia WGS AF: 0.158 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.2
DANN	Benign	0.37
PhyloP100		0.080

Splicing

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

Other links and lift over

dbSNP: rs397703; hg19: chr13-33587329;