11-127463945-G-C

Variant names:

• chr11-127463945-G-C
• rs1881470
• ENST00000822754.1:n.233-30345G>C

Variant summary

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

The ENST00000822754.1(ENSG00000307024):​n.233-30345G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,078 control chromosomes in the GnomAD database, including 9,720 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 0.33 (9720 hom., cov: 32)
• Consequence: ENSG00000307024 ENST00000822754.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 1 publications found

Genes affected

ENSG00000307024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984373	XR_001748081.2	n.128-30345G>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307024	ENST00000822754.1	n.233-30345G>C		intron_variant	Intron 2 of 3
ENSG00000307024	ENST00000822755.1	n.270-32217G>C		intron_variant	Intron 2 of 2
ENSG00000307024	ENST00000822756.1	n.224-32217G>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50151 AN: 151960 Hom.: 9697 Cov.: 32

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.330 AC: 50214 AN: 152078 Hom.: 9720 Cov.: 32 AF XY: 0.330 AC XY: 24506 AN XY: 74334

African (AFR) AF: 0.545 AC: 22588 AN: 41468

American (AMR) AF: 0.240 AC: 3676 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 867 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1119 AN: 5170

South Asian (SAS) AF: 0.388 AC: 1869 AN: 4820

European-Finnish (FIN) AF: 0.260 AC: 2754 AN: 10578

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16480 AN: 67972

Other (OTH) AF: 0.296 AC: 625 AN: 2108

Alfa AF: 0.0921 Hom.: 129

Bravo AF: 0.336

Asia WGS AF: 0.367 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.73
DANN	Benign	0.33
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1881470; hg19: chr11-127333840;