rs12518350

Positions:

• chr5-130760567-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661392.1(ENSG00000287390):​n.348+37972T>C variant causes a intron, non coding transcript 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: ENST00000661392.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.665

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661392.1	n.348+37972T>C		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.370

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.437

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.265

Gnomad4 OTH AF: 0.285

Alfa AF: 0.272 Hom.: 11841

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12518350; hg19: chr5-130096260;