12-41905080-C-T

Position:

• chr12-41905080-C-T

Variant summary

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

The ENST00000550874.1(ENSG00000257239):​n.471+27042G>A 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 0.1 in 151,358 control chromosomes in the GnomAD database, including 937 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 0.10 (937 hom., cov: 31)
• Consequence: ENST00000550874.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000550874.1	n.471+27042G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15182 AN: 151248 Hom.: 939 Cov.: 31

Gnomad AFR AF: 0.0307

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0987

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.100 AC: 15170 AN: 151358 Hom.: 937 Cov.: 31 AF XY: 0.100 AC XY: 7384 AN XY: 73862

Gnomad4 AFR AF: 0.0306

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.163

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.0985

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.111

Alfa AF: 0.126 Hom.: 2660

Bravo AF: 0.0964

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.7
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491998; hg19: chr12-42298882;