rs12518350

Variant names:

• chr5-130760567-A-G
• rs12518350
• ENST00000661392.1:n.348+37972T>C

Variant summary

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

The ENST00000661392.1(ENSG00000287390):​n.348+37972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,070 control chromosomes in the GnomAD database, including 7,274 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 0.30 (7274 hom., cov: 32)
• Consequence: ENSG00000287390 ENST00000661392.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665
• Publications: 3 publications found

Genes affected

ENSG00000287390 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.422 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
ENSG00000287390	ENST00000661392.1	n.348+37972T>C		intron_variant	Intron 4 of 5
ENSG00000287390	ENST00000804525.1	n.450+37972T>C		intron_variant	Intron 4 of 4
ENSG00000287390	ENST00000804527.1	n.469+37972T>C		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46262 AN: 151952 Hom.: 7249 Cov.: 32

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.384

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.265

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.305 AC: 46336 AN: 152070 Hom.: 7274 Cov.: 32 AF XY: 0.312 AC XY: 23190 AN XY: 74326

African (AFR) AF: 0.318 AC: 13208 AN: 41488

American (AMR) AF: 0.370 AC: 5650 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 971 AN: 3468

East Asian (EAS) AF: 0.437 AC: 2259 AN: 5168

South Asian (SAS) AF: 0.385 AC: 1856 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3638 AN: 10568

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.265 AC: 17994 AN: 67968

Other (OTH) AF: 0.285 AC: 601 AN: 2110

Alfa AF: 0.278 Hom.: 20381

Bravo AF: 0.305

Asia WGS AF: 0.444 AC: 1547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	8.6
DANN	Benign	0.82
PhyloP100		0.67

Splicing

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

Other links and lift over

dbSNP: rs12518350; hg19: chr5-130096260;