rs7118530

Variant names:

• chr11-114019403-T-C
• rs7118530
• ENST00000770045.1:n.226-15859T>C

Variant summary

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

The ENST00000770045.1(ENSG00000300211):​n.226-15859T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 152,102 control chromosomes in the GnomAD database, including 7,782 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 0.31 (7782 hom., cov: 33)
• Consequence: ENSG00000300211 ENST00000770045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270
• Publications: 5 publications found

Genes affected

ENSG00000300211 (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 (SAS) allele frequency at 95% confidence interval = 0.351 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
ENSG00000300211	ENST00000770045.1	n.226-15859T>C		intron_variant	Intron 2 of 3
ENSG00000300211	ENST00000770046.1	n.140+3910T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47557 AN: 151984 Hom.: 7781 Cov.: 33

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.303

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.354

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.313 AC: 47571 AN: 152102 Hom.: 7782 Cov.: 33 AF XY: 0.311 AC XY: 23152 AN XY: 74360

African (AFR) AF: 0.238 AC: 9880 AN: 41466

American (AMR) AF: 0.307 AC: 4701 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1290 AN: 3470

East Asian (EAS) AF: 0.303 AC: 1563 AN: 5156

South Asian (SAS) AF: 0.358 AC: 1725 AN: 4820

European-Finnish (FIN) AF: 0.296 AC: 3136 AN: 10600

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.354 AC: 24087 AN: 67980

Other (OTH) AF: 0.340 AC: 718 AN: 2112

Alfa AF: 0.344 Hom.: 38748

Bravo AF: 0.309

Asia WGS AF: 0.290 AC: 1008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.5
DANN	Benign	0.57
PhyloP100		0.027

Splicing

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

Other links and lift over

dbSNP: rs7118530; hg19: chr11-113890125;