12-91618424-T-C

Position:

• chr12-91618424-T-C

Variant summary

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

The ENST00000685093.1(ENSG00000289605):​n.503+15301A>G 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 0.397 in 152,098 control chromosomes in the GnomAD database, including 12,052 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 0.40 (12052 hom., cov: 32)
• Consequence: ENST00000685093.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0570

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105369896	XR_001749251.2	n.3670+15301A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000685093.1	n.503+15301A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60289 AN: 151980 Hom.: 12042 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.397 AC: 60349 AN: 152098 Hom.: 12052 Cov.: 32 AF XY: 0.394 AC XY: 29304 AN XY: 74368

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.341

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.403

Alfa AF: 0.396 Hom.: 19566

Bravo AF: 0.407

Asia WGS AF: 0.497 AC: 1729 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	2.2
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1489895; hg19: chr12-92012201;