ENST00000724020.1:n.163-23575C>A

Variant names:

• chr4-186796763-C-A
• rs1431935
• ENST00000724020.1:n.163-23575C>A

Variant summary

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

Score: -12 - Benign

-12

BP4_StrongBA1

The ENST00000724020.1(ENSG00000294511):​n.163-23575C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,792 control chromosomes in the GnomAD database, including 12,876 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 0.39 (12876 hom., cov: 32)
• Consequence: ENSG00000294511 ENST00000724020.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.51
• Publications: 1 publications found

Genes affected

ENSG00000294511 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.49 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
ENSG00000294511	ENST00000724020.1	n.163-23575C>A		intron_variant	Intron 1 of 1
ENSG00000294511	ENST00000724021.1	n.127-6055C>A		intron_variant	Intron 1 of 2
ENSG00000294511	ENST00000724022.1	n.81-6055C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59206 AN: 151674 Hom.: 12876 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.597

Gnomad EAS AF: 0.319

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.448

Gnomad MID AF: 0.436

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.390 AC: 59213 AN: 151792 Hom.: 12876 Cov.: 32 AF XY: 0.389 AC XY: 28874 AN XY: 74166

African (AFR) AF: 0.189 AC: 7819 AN: 41368

American (AMR) AF: 0.408 AC: 6239 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.597 AC: 2073 AN: 3470

East Asian (EAS) AF: 0.319 AC: 1649 AN: 5162

South Asian (SAS) AF: 0.387 AC: 1859 AN: 4804

European-Finnish (FIN) AF: 0.448 AC: 4699 AN: 10486

Middle Eastern (MID) AF: 0.418 AC: 122 AN: 292

European-Non Finnish (NFE) AF: 0.494 AC: 33561 AN: 67912

Other (OTH) AF: 0.434 AC: 916 AN: 2112

Alfa AF: 0.440 Hom.: 5620

Bravo AF: 0.377

Asia WGS AF: 0.345 AC: 1201 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	10
DANN	Benign	0.41
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs1431935; hg19: chr4-187717917;