rs12916483

Variant names:

• chr15-78540055-G-A
• rs12916483
• ENST00000746668.1:n.130+161C>T

Variant summary

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

The ENST00000746668.1(ENSG00000297264):​n.130+161C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 152,152 control chromosomes in the GnomAD database, including 8,578 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 0.32 (8578 hom., cov: 32)
• Consequence: ENSG00000297264 ENST00000746668.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.463
• Publications: 16 publications found

Genes affected

ENSG00000297264 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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
ENSG00000297264	ENST00000746668.1	n.130+161C>T		intron_variant	Intron 1 of 2
ENSG00000297264	ENST00000746669.1	n.107+161C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47925 AN: 152034 Hom.: 8581 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.433

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.371

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.316

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

GnomAD4 genome AF: 0.315 AC: 47934 AN: 152152 Hom.: 8578 Cov.: 32 AF XY: 0.312 AC XY: 23234 AN XY: 74394

African (AFR) AF: 0.162 AC: 6742 AN: 41524

American (AMR) AF: 0.249 AC: 3808 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1227 AN: 3470

East Asian (EAS) AF: 0.165 AC: 854 AN: 5178

South Asian (SAS) AF: 0.341 AC: 1644 AN: 4818

European-Finnish (FIN) AF: 0.371 AC: 3927 AN: 10574

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28606 AN: 67976

Other (OTH) AF: 0.317 AC: 671 AN: 2114

Alfa AF: 0.374 Hom.: 14584

Bravo AF: 0.299

Asia WGS AF: 0.271 AC: 941 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	6.7
DANN	Benign	0.56
PhyloP100		0.46
PromoterAI		0.056	Neutral

Splicing

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

Other links and lift over

dbSNP: rs12916483; hg19: chr15-78832397;