rs12418774

Variant names:

• chr11-68006761-A-G
• rs12418774
• ENST00000840914.1:n.488A>G

Variant summary

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

The ENST00000840914.1(ENSG00000309414):​n.488A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.084 in 152,122 control chromosomes in the GnomAD database, including 686 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 0.084 (686 hom., cov: 32)
• Consequence: ENSG00000309414 ENST00000840914.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151
• Publications: 4 publications found

Genes affected

ENSG00000309414 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000309414	ENST00000840914.1	n.488A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000309414	ENST00000840917.1	n.430A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000309414	ENST00000840918.1	n.367A>G		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0840 AC: 12774 AN: 152004 Hom.: 686 Cov.: 32

Gnomad AFR AF: 0.0411

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.0808

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0139

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0666

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.0966

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

GnomAD4 genome AF: 0.0840 AC: 12775 AN: 152122 Hom.: 686 Cov.: 32 AF XY: 0.0808 AC XY: 6012 AN XY: 74384

African (AFR) AF: 0.0410 AC: 1702 AN: 41512

American (AMR) AF: 0.0806 AC: 1231 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 458 AN: 3472

East Asian (EAS) AF: 0.0139 AC: 72 AN: 5162

South Asian (SAS) AF: 0.108 AC: 521 AN: 4812

European-Finnish (FIN) AF: 0.0666 AC: 706 AN: 10596

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.112 AC: 7634 AN: 67972

Other (OTH) AF: 0.0951 AC: 201 AN: 2114

Alfa AF: 0.0995 Hom.: 616

Bravo AF: 0.0825

Asia WGS AF: 0.0590 AC: 205 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	1.9
DANN	Benign	0.67
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12418774; hg19: chr11-67774231;