rs1349411

Variant names:

• chr12-7240062-C-T
• rs1349411

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: LOC100420983 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 6 publications found

Genes affected

LOC100420983 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000540190.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000256480	ENST00000540190.1	TSL:6	n.107-793C>T		intron	N/A

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

African (AFR) AF: 0.468 AC: 19390 AN: 41448

American (AMR) AF: 0.570 AC: 8698 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1559 AN: 3472

East Asian (EAS) AF: 0.779 AC: 4031 AN: 5174

South Asian (SAS) AF: 0.739 AC: 3568 AN: 4826

European-Finnish (FIN) AF: 0.431 AC: 4548 AN: 10542

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30706 AN: 67962

Other (OTH) AF: 0.475 AC: 1003 AN: 2112

Alfa AF: 0.462 Hom.: 28221

Bravo AF: 0.493

Asia WGS AF: 0.691 AC: 2402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.70
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1349411; hg19: chr12-7392658;