rs11159518

Variant names:

• chr14-81964767-A-G
• rs11159518
• ENST00000554814.1:n.316-65339A>G

Your query was ambiguous. Multiple possible variants found:

• chr14-81964767-A-G
• chr14-81964767-A-T

Variant summary

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

The ENST00000554814.1(ENSG00000259035):​n.316-65339A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 151,914 control chromosomes in the GnomAD database, including 7,389 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 0.30 (7389 hom., cov: 32)
• Consequence: ENSG00000259035 ENST00000554814.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.579
• Publications: 4 publications found

Genes affected

ENSG00000259035 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554814.1. 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
	ENSG00000259035	ENST00000554814.1	TSL:4	n.316-65339A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45572 AN: 151796 Hom.: 7375 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.300 AC: 45618 AN: 151914 Hom.: 7389 Cov.: 32 AF XY: 0.304 AC XY: 22555 AN XY: 74224

African (AFR) AF: 0.172 AC: 7151 AN: 41470

American (AMR) AF: 0.339 AC: 5161 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1267 AN: 3470

East Asian (EAS) AF: 0.383 AC: 1962 AN: 5126

South Asian (SAS) AF: 0.374 AC: 1802 AN: 4814

European-Finnish (FIN) AF: 0.363 AC: 3834 AN: 10564

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23270 AN: 67914

Other (OTH) AF: 0.342 AC: 723 AN: 2114

Alfa AF: 0.331 Hom.: 33710

Bravo AF: 0.293

Asia WGS AF: 0.386 AC: 1341 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.67
PhyloP100		-0.58

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11159518;

hg19: chr14-82431111;