4-154556220-T-A

Variant names:

• chr4-154556220-T-A
• rs12648258
• ENST00000507985.1:n.*235T>A

Variant summary

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

The ENST00000507985.1(ENSG00000248611):​n.*235T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,126 control chromosomes in the GnomAD database, including 3,199 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 0.18 (3199 hom., cov: 32)
• Consequence: ENSG00000248611 ENST00000507985.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 1 publications found

Genes affected

ENSG00000248611 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.531 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000507985.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248611	ENST00000507985.1	TSL:6	n.*235T>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26843 AN: 152008 Hom.: 3201 Cov.: 32

Gnomad AFR AF: 0.0523

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.548

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.176 AC: 26840 AN: 152126 Hom.: 3199 Cov.: 32 AF XY: 0.183 AC XY: 13620 AN XY: 74372

African (AFR) AF: 0.0522 AC: 2168 AN: 41530

American (AMR) AF: 0.208 AC: 3181 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.139 AC: 482 AN: 3470

East Asian (EAS) AF: 0.548 AC: 2833 AN: 5168

South Asian (SAS) AF: 0.244 AC: 1176 AN: 4816

European-Finnish (FIN) AF: 0.258 AC: 2733 AN: 10580

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13578 AN: 67980

Other (OTH) AF: 0.171 AC: 360 AN: 2104

Alfa AF: 0.181 Hom.: 372

Bravo AF: 0.169

Asia WGS AF: 0.340 AC: 1180 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.82
DANN	Benign	0.22
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs12648258; hg19: chr4-155477372;