rs12930287

Variant names:

• chr16-65904503-G-A
• rs12930287
• ENST00000739848.1:n.363+14553C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000739848.1(ENSG00000296480):​n.363+14553C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0314 in 152,262 control chromosomes in the GnomAD database, including 118 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 0.031 (118 hom., cov: 32)
• Consequence: ENSG00000296480 ENST00000739848.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.134
• Publications: 2 publications found

Genes affected

ENSG00000296480 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.6).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0314 (4785/152262) while in subpopulation NFE AF = 0.047 (3195/68022). AF 95% confidence interval is 0.0456. There are 118 homozygotes in GnomAd4. There are 2288 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 118 gene

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
ENSG00000296480	ENST00000739848.1	n.363+14553C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0314 AC: 4782 AN: 152144 Hom.: 118 Cov.: 32

Gnomad AFR AF: 0.00825

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0276

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0270

Gnomad FIN AF: 0.0444

Gnomad MID AF: 0.00318

Gnomad NFE AF: 0.0470

Gnomad OTH AF: 0.0177

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

GnomAD4 genome AF: 0.0314 AC: 4785 AN: 152262 Hom.: 118 Cov.: 32 AF XY: 0.0307 AC XY: 2288 AN XY: 74436

African (AFR) AF: 0.00823 AC: 342 AN: 41552

American (AMR) AF: 0.0276 AC: 422 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5188

South Asian (SAS) AF: 0.0274 AC: 132 AN: 4814

European-Finnish (FIN) AF: 0.0444 AC: 471 AN: 10598

Middle Eastern (MID) AF: 0.00342 AC: 1 AN: 292

European-Non Finnish (NFE) AF: 0.0470 AC: 3195 AN: 68022

Other (OTH) AF: 0.0175 AC: 37 AN: 2114

Alfa AF: 0.0367 Hom.: 87

Bravo AF: 0.0303

Asia WGS AF: 0.0140 AC: 50 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.60
CADD	Benign	7.5
DANN	Benign	0.78
PhyloP100		0.13

Splicing

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

Other links and lift over

dbSNP: rs12930287; hg19: chr16-65938406;