chr4-23055287-A-C

Variant names:

• chr4-23055287-A-C
• rs1394022
• ENST00000511453.5:n.286-552A>C

Variant summary

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

The ENST00000511453.5(ENSG00000248837):​n.286-552A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0407 in 152,158 control chromosomes in the GnomAD database, including 337 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 0.041 (337 hom., cov: 32)
• Consequence: ENSG00000248837 ENST00000511453.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 0 publications found

Genes affected

ENSG00000248837 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.124 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374524	XR_007058432.1	n.305-28410A>C		intron_variant	Intron 3 of 7
LOC105374524	XR_007058433.1	n.305-28410A>C		intron_variant	Intron 3 of 7
LOC105374524	XR_007058434.1	n.305-28410A>C		intron_variant	Intron 3 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000248837	ENST00000511453.5	n.286-552A>C		intron_variant	Intron 3 of 3	3
ENSG00000248837	ENST00000652324.1	n.302-28410A>C		intron_variant	Intron 3 of 9
ENSG00000248837	ENST00000653008.1	n.431+14505A>C		intron_variant	Intron 5 of 9

Frequencies

GnomAD3 genomes AF: 0.0407 AC: 6190 AN: 152038 Hom.: 338 Cov.: 32

Gnomad AFR AF: 0.127

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0182

Gnomad ASJ AF: 0.0110

Gnomad EAS AF: 0.0143

Gnomad SAS AF: 0.0247

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00557

Gnomad OTH AF: 0.0292

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

GnomAD4 genome AF: 0.0407 AC: 6200 AN: 152158 Hom.: 337 Cov.: 32 AF XY: 0.0397 AC XY: 2954 AN XY: 74386

African (AFR) AF: 0.126 AC: 5247 AN: 41508

American (AMR) AF: 0.0182 AC: 278 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0110 AC: 38 AN: 3468

East Asian (EAS) AF: 0.0143 AC: 74 AN: 5172

South Asian (SAS) AF: 0.0247 AC: 119 AN: 4818

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10608

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00556 AC: 378 AN: 67998

Other (OTH) AF: 0.0289 AC: 61 AN: 2108

Alfa AF: 0.0223 Hom.: 34

Bravo AF: 0.0446

Asia WGS AF: 0.0290 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.92
DANN	Benign	0.62
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1394022; hg19: chr4-23056910;