rs13273073

Variant names:

• chr8-23726713-G-T
• rs13273073
• ENST00000686210.2:n.423C>A

Variant summary

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

The ENST00000686210.2(ENSG00000254002):​n.423C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,210 control chromosomes in the GnomAD database, including 4,830 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 0.24 (4828 hom., cov: 32)
  • Exomes 𝑓: 0.21 (2 hom.)
• Consequence: ENSG00000254002 ENST00000686210.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 9 publications found

Genes affected

ENSG00000254002 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000686210.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101929258	NR_188036.1		n.94-102C>A		intron	N/A
	LOC101929258	NR_188037.1		n.94-102C>A		intron	N/A
	LOC101929258	NR_188038.1		n.94-102C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254002	ENST00000686210.2		n.423C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000254002	ENST00000702219.2		n.302C>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000254002	ENST00000520375.1	TSL:3	n.163-102C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37215 AN: 152000 Hom.: 4824 Cov.: 32

Gnomad AFR AF: 0.288

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.264

GnomAD4 exome AF: 0.207 AC: 19 AN: 92 Hom.: 2 AF XY: 0.197 AC XY: 13 AN XY: 66

African (AFR) AC: 0 AN: 0

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.375 AC: 3 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.191 AC: 13 AN: 68

Other (OTH) AF: 0.167 AC: 1 AN: 6

GnomAD4 genome AF: 0.245 AC: 37254 AN: 152118 Hom.: 4828 Cov.: 32 AF XY: 0.242 AC XY: 18007 AN XY: 74364

African (AFR) AF: 0.288 AC: 11966 AN: 41482

American (AMR) AF: 0.189 AC: 2886 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1037 AN: 3470

East Asian (EAS) AF: 0.0822 AC: 425 AN: 5170

South Asian (SAS) AF: 0.337 AC: 1621 AN: 4810

European-Finnish (FIN) AF: 0.211 AC: 2234 AN: 10594

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16279 AN: 67980

Other (OTH) AF: 0.265 AC: 559 AN: 2112

Alfa AF: 0.242 Hom.: 19691

Bravo AF: 0.243

Asia WGS AF: 0.264 AC: 916 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	7.6
DANN	Benign	0.88
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs13273073; hg19: chr8-23584226;