ENST00000840914.1:n.168-14G>A

Variant names:

• chr11-68006427-G-A
• rs7952122
• ENST00000840914.1:n.168-14G>A

Variant summary

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

The ENST00000840914.1(ENSG00000309414):​n.168-14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 151,926 control chromosomes in the GnomAD database, including 4,504 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 0.23 (4504 hom., cov: 31)
• Consequence: ENSG00000309414 ENST00000840914.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 9 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.347 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.168-14G>A		intron_variant	Intron 1 of 1
ENSG00000309414	ENST00000840915.1	n.526-14G>A		intron_variant	Intron 1 of 1
ENSG00000309414	ENST00000840916.1	n.399-14G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34765 AN: 151808 Hom.: 4502 Cov.: 31

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0903

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.229 AC: 34801 AN: 151926 Hom.: 4504 Cov.: 31 AF XY: 0.221 AC XY: 16379 AN XY: 74250

African (AFR) AF: 0.351 AC: 14529 AN: 41352

American (AMR) AF: 0.161 AC: 2456 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3470

East Asian (EAS) AF: 0.203 AC: 1048 AN: 5162

South Asian (SAS) AF: 0.127 AC: 613 AN: 4816

European-Finnish (FIN) AF: 0.0903 AC: 954 AN: 10562

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.203 AC: 13811 AN: 67970

Other (OTH) AF: 0.228 AC: 480 AN: 2106

Alfa AF: 0.213 Hom.: 10038

Bravo AF: 0.240

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.47
DANN	Benign	0.61
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs7952122; hg19: chr11-67773897;