rs1349411

Positions:

• chr12-7240062-C-T

Variant summary

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

The ENST00000540190.1(ENSG00000256480):​n.107-793C>T 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 0.488 in 152,000 control chromosomes in the GnomAD database, including 18,664 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 0.49 (18664 hom., cov: 32)
• Consequence: ENST00000540190.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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
	ENST00000540190.1	n.107-793C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74070 AN: 151880 Hom.: 18632 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.431

Gnomad MID AF: 0.506

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.488 AC: 74159 AN: 152000 Hom.: 18664 Cov.: 32 AF XY: 0.494 AC XY: 36664 AN XY: 74290

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.570

Gnomad4 ASJ AF: 0.449

Gnomad4 EAS AF: 0.779

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.431

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.475

Alfa AF: 0.460 Hom.: 17950

Bravo AF: 0.493

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1349411; hg19: chr12-7392658;