rs729239

Variant names:

• chr4-77142243-G-A
• rs729239
• ENST00000721175.1:n.191-2473G>A

Variant summary

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

The ENST00000721175.1(ENSG00000289496):​n.191-2473G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 152,130 control chromosomes in the GnomAD database, including 2,014 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 0.13 (2014 hom., cov: 32)
• Consequence: ENSG00000289496 ENST00000721175.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 2 publications found

Genes affected

ENSG00000289496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289496	ENST00000721175.1	n.191-2473G>A		intron_variant	Intron 1 of 2
ENSG00000289496	ENST00000721176.1	n.284-2473G>A		intron_variant	Intron 2 of 3
ENSG00000289496	ENST00000721177.1	n.258-8994G>A		intron_variant	Intron 2 of 2
ENSG00000289496	ENST00000721178.1	n.348-8994G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19823 AN: 152012 Hom.: 2003 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0863

Gnomad ASJ AF: 0.0565

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.0767

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0770

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.131 AC: 19880 AN: 152130 Hom.: 2014 Cov.: 32 AF XY: 0.126 AC XY: 9396 AN XY: 74396

African (AFR) AF: 0.283 AC: 11735 AN: 41460

American (AMR) AF: 0.0861 AC: 1316 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0565 AC: 196 AN: 3470

East Asian (EAS) AF: 0.0389 AC: 201 AN: 5172

South Asian (SAS) AF: 0.0774 AC: 373 AN: 4818

European-Finnish (FIN) AF: 0.0401 AC: 424 AN: 10586

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0770 AC: 5235 AN: 68016

Other (OTH) AF: 0.113 AC: 239 AN: 2116

Alfa AF: 0.124 Hom.: 309

Bravo AF: 0.141

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.010
DANN	Benign	0.38
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs729239; hg19: chr4-78063396;