ENST00000527543.3:n.337-7783G>A

Variant names:

• chr11-67947557-C-T
• rs308309
• ENST00000527543.3:n.337-7783G>A

Variant summary

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

The ENST00000527543.3(ENSG00000290995):​n.337-7783G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 152,138 control chromosomes in the GnomAD database, including 49,342 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 0.80 (49342 hom., cov: 33)
• Consequence: ENSG00000290995 ENST00000527543.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• Publications: 8 publications found

Genes affected

ENSG00000290995 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268076	XM_047427952.1	c.897+7925G>A		intron_variant	Intron 3 of 3		XP_047283908.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290995	ENST00000527543.3	n.337-7783G>A		intron_variant	Intron 1 of 3	5
ENSG00000290995	ENST00000763345.1	n.367+7925G>A		intron_variant	Intron 1 of 2
ENSG00000290995	ENST00000763346.1	n.324+7925G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122191 AN: 152018 Hom.: 49294 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.793

Gnomad EAS AF: 0.831

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.790

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.818

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

GnomAD4 genome AF: 0.804 AC: 122297 AN: 152138 Hom.: 49342 Cov.: 33 AF XY: 0.806 AC XY: 59969 AN XY: 74382

African (AFR) AF: 0.878 AC: 36469 AN: 41528

American (AMR) AF: 0.809 AC: 12357 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.793 AC: 2753 AN: 3470

East Asian (EAS) AF: 0.831 AC: 4259 AN: 5126

South Asian (SAS) AF: 0.806 AC: 3887 AN: 4820

European-Finnish (FIN) AF: 0.790 AC: 8366 AN: 10596

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.758 AC: 51578 AN: 68002

Other (OTH) AF: 0.821 AC: 1732 AN: 2110

Alfa AF: 0.776 Hom.: 179678

Bravo AF: 0.810

Asia WGS AF: 0.825 AC: 2869 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	4.9
DANN	Benign	0.52
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs308309; hg19: chr11-67715028;