12-41916107-T-C

Variant summary

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

The ENST00000550874.1(ENSG00000257239):n.471+16015A>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 0.544 in 152,000 control chromosomes in the GnomAD database, including 23,475 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 0.54 (23475 hom., cov: 32)
• Consequence: ENST00000550874.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.211

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.611 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
	ENST00000550874.1	n.471+16015A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82710 AN: 151882 Hom.: 23462 Cov.: 32

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.541

Gnomad AMR AF: 0.557

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.616

Gnomad OTH AF: 0.558

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

GnomAD4 genome AF: 0.544 AC: 82755 AN: 152000 Hom.: 23475 Cov.: 32 AF XY: 0.545 AC XY: 40499 AN XY: 74294

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.557

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.594

Gnomad4 SAS AF: 0.602

Gnomad4 FIN AF: 0.638

Gnomad4 NFE AF: 0.616

Gnomad4 OTH AF: 0.561

Alfa AF: 0.577 Hom.: 3920

Bravo AF: 0.529

Asia WGS AF: 0.589 AC: 2050 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	6.4
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2215456; hg19: chr12-42309909; COSMIC: COSV73441619;