chr12-53865917-G-A

Variant names:

• chr12-53865917-G-A
• rs7306498
• ENST00000652339.1:n.509+5039G>A

Variant summary

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

The ENST00000652339.1(ENSG00000286069):​n.509+5039G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 151,974 control chromosomes in the GnomAD database, including 10,041 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 0.36 (10041 hom., cov: 31)
• Consequence: ENSG00000286069 ENST00000652339.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 3 publications found

Genes affected

ENSG00000286069 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.404 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378250	NR_189097.1	n.398+15505G>A		intron_variant	Intron 2 of 2
LOC105378250	NR_189098.1	n.497-9238G>A		intron_variant	Intron 3 of 4
LOC105378250	NR_189099.1	n.591+5039G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286069	ENST00000652339.1	n.509+5039G>A		intron_variant	Intron 4 of 4
ENSG00000286069	ENST00000654713.2	n.317+15505G>A		intron_variant	Intron 2 of 2
ENSG00000286069	ENST00000656247.1	n.344+15505G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54440 AN: 151856 Hom.: 10039 Cov.: 31

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.408

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.358 AC: 54451 AN: 151974 Hom.: 10041 Cov.: 31 AF XY: 0.351 AC XY: 26099 AN XY: 74294

African (AFR) AF: 0.333 AC: 13794 AN: 41444

American (AMR) AF: 0.262 AC: 3995 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1459 AN: 3470

East Asian (EAS) AF: 0.230 AC: 1184 AN: 5158

South Asian (SAS) AF: 0.359 AC: 1728 AN: 4820

European-Finnish (FIN) AF: 0.320 AC: 3377 AN: 10554

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.408 AC: 27744 AN: 67954

Other (OTH) AF: 0.337 AC: 712 AN: 2114

Alfa AF: 0.283 Hom.: 1035

Bravo AF: 0.350

Asia WGS AF: 0.288 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.39
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7306498; hg19: chr12-54259701;