4-28344153-T-C

Variant names:

• chr4-28344153-T-C
• rs2036184
• ENST00000651324.2:n.648-261A>G

Variant summary

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

The ENST00000651324.2(ENSG00000250038):​n.648-261A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,816 control chromosomes in the GnomAD database, including 22,448 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 0.54 (22448 hom., cov: 31)
• Consequence: ENSG00000250038 ENST00000651324.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.787
• Publications: 3 publications found

Genes affected

ENSG00000250038 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374557	NR_188396.1	n.287+129005T>C		intron_variant	Intron 2 of 4
LOC105374557	NR_188397.1	n.287+129005T>C		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250038	ENST00000651324.2	n.648-261A>G		intron_variant	Intron 4 of 5
ENSG00000250038	ENST00000772476.1	n.253+26547A>G		intron_variant	Intron 2 of 4
ENSG00000250038	ENST00000772477.1	n.553-261A>G		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81754 AN: 151698 Hom.: 22423 Cov.: 31

Gnomad AFR AF: 0.531

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.534

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.632

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.539 AC: 81827 AN: 151816 Hom.: 22448 Cov.: 31 AF XY: 0.546 AC XY: 40519 AN XY: 74210

African (AFR) AF: 0.531 AC: 21955 AN: 41376

American (AMR) AF: 0.659 AC: 10042 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 1853 AN: 3470

East Asian (EAS) AF: 0.713 AC: 3671 AN: 5146

South Asian (SAS) AF: 0.632 AC: 3039 AN: 4812

European-Finnish (FIN) AF: 0.593 AC: 6257 AN: 10548

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33391 AN: 67918

Other (OTH) AF: 0.548 AC: 1155 AN: 2106

Alfa AF: 0.510 Hom.: 68000

Bravo AF: 0.541

Asia WGS AF: 0.682 AC: 2369 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.19
DANN	Benign	0.63
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs2036184; hg19: chr4-28345775;