rs13147758

Variant names:

• chr4-144539078-A-G
• rs13147758
• ENST00000649263.1:n.328-123100T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-123100T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,120 control chromosomes in the GnomAD database, including 9,456 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as association (no stars).

• Frequency: Genomes: 𝑓 0.32 (9456 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: association no assertion criteria provided O:2
• Conservation: PhyloP100: 1.53
• Publications: 42 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.474 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. 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
	ENSG00000285713	ENST00000649263.1		n.328-123100T>C		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.223-123100T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48459 AN: 152000 Hom.: 9447 Cov.: 32

Gnomad AFR AF: 0.0952

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.319 AC: 48474 AN: 152120 Hom.: 9456 Cov.: 32 AF XY: 0.326 AC XY: 24220 AN XY: 74334

African (AFR) AF: 0.0950 AC: 3948 AN: 41538

American (AMR) AF: 0.311 AC: 4748 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1140 AN: 3472

East Asian (EAS) AF: 0.301 AC: 1551 AN: 5160

South Asian (SAS) AF: 0.491 AC: 2366 AN: 4822

European-Finnish (FIN) AF: 0.536 AC: 5655 AN: 10544

Middle Eastern (MID) AF: 0.363 AC: 106 AN: 292

European-Non Finnish (NFE) AF: 0.411 AC: 27962 AN: 67984

Other (OTH) AF: 0.303 AC: 640 AN: 2112

Alfa AF: 0.382 Hom.: 36268

Bravo AF: 0.285

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

ClinVar submissions

Significance: association

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	-	Chronic obstructive pulmonary disease (1)
-	-	-	Chronic obstructive pulmonary disease, biomass related (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.8
DANN	Benign	0.35
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs13147758; hg19: chr4-145460230;