rs7315280

Variant names:

• chr12-116883133-A-G
• rs7315280
• ENST00000752207.1:n.111+4365A>G

Variant summary

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

The ENST00000752207.1(ENSG00000297968):​n.111+4365A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,062 control chromosomes in the GnomAD database, including 3,497 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 0.19 (3497 hom., cov: 32)
• Consequence: ENSG00000297968 ENST00000752207.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.818
• Publications: 9 publications found

Genes affected

ENSG00000297968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 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
ENSG00000297968	ENST00000752207.1	n.111+4365A>G		intron_variant	Intron 1 of 1
ENSG00000297968	ENST00000752208.1	n.84+4365A>G		intron_variant	Intron 1 of 2
ENSG00000297968	ENST00000752209.1	n.83+4365A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28285 AN: 151944 Hom.: 3494 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0693

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0833

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.186 AC: 28322 AN: 152062 Hom.: 3497 Cov.: 32 AF XY: 0.182 AC XY: 13513 AN XY: 74328

African (AFR) AF: 0.361 AC: 14953 AN: 41438

American (AMR) AF: 0.142 AC: 2165 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3470

East Asian (EAS) AF: 0.0693 AC: 358 AN: 5166

South Asian (SAS) AF: 0.103 AC: 496 AN: 4816

European-Finnish (FIN) AF: 0.0833 AC: 882 AN: 10584

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

European-Non Finnish (NFE) AF: 0.120 AC: 8157 AN: 67982

Other (OTH) AF: 0.195 AC: 412 AN: 2116

Alfa AF: 0.147 Hom.: 5719

Bravo AF: 0.200

Asia WGS AF: 0.103 AC: 357 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	16
DANN	Benign	0.70
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs7315280; hg19: chr12-117320938;