rs12648258

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr4-154556220-T-A
• chr4-154556220-T-C
• chr4-154556220-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000248611 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000248611	ENST00000507985.1	n.*235T>A		downstream_gene_variant		6

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

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.208

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.548

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.171

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12648258; hg19: chr4-155477372;