rs12148658

Variant names:

• chr15-37876078-G-A
• rs12148658
• ENST00000772735.1:n.387+28269C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000772735.1(ENSG00000300563):​n.387+28269C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,044 control chromosomes in the GnomAD database, including 860 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 0.097 (860 hom., cov: 32)
• Consequence: ENSG00000300563 ENST00000772735.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.17
• Publications: 5 publications found

Genes affected

ENSG00000300563 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 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
ENSG00000300563	ENST00000772735.1	n.387+28269C>T		intron_variant	Intron 3 of 4
ENSG00000300563	ENST00000772736.1	n.354+28269C>T		intron_variant	Intron 3 of 4
ENSG00000300563	ENST00000772737.1	n.424+28269C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14760 AN: 151926 Hom.: 861 Cov.: 32

Gnomad AFR AF: 0.0504

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.0850

Gnomad EAS AF: 0.0248

Gnomad SAS AF: 0.0969

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0971 AC: 14763 AN: 152044 Hom.: 860 Cov.: 32 AF XY: 0.0996 AC XY: 7401 AN XY: 74304

African (AFR) AF: 0.0504 AC: 2093 AN: 41518

American (AMR) AF: 0.104 AC: 1589 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0850 AC: 295 AN: 3470

East Asian (EAS) AF: 0.0247 AC: 127 AN: 5140

South Asian (SAS) AF: 0.0972 AC: 469 AN: 4826

European-Finnish (FIN) AF: 0.156 AC: 1647 AN: 10578

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8250 AN: 67936

Other (OTH) AF: 0.112 AC: 236 AN: 2110

Alfa AF: 0.122 Hom.: 688

Bravo AF: 0.0901

Asia WGS AF: 0.0600 AC: 209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.43
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs12148658; hg19: chr15-38168279;