rs11153730

Variant names:

• chr6-118346359-T-C
• rs11153730
• ENST00000778490.1:n.618-45026A>G

Variant summary

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

The ENST00000778490.1(ENSG00000301363):​n.618-45026A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 152,158 control chromosomes in the GnomAD database, including 12,835 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 0.40 (12835 hom., cov: 33)
• Consequence: ENSG00000301363 ENST00000778490.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.808
• Publications: 65 publications found

Genes affected

ENSG00000301363 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.487 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
ENSG00000301363	ENST00000778490.1	n.618-45026A>G		intron_variant	Intron 1 of 1
ENSG00000301363	ENST00000778491.1	n.159-21172A>G		intron_variant	Intron 1 of 3
ENSG00000301363	ENST00000778492.1	n.622-22176A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60475 AN: 152040 Hom.: 12837 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.398 AC: 60501 AN: 152158 Hom.: 12835 Cov.: 33 AF XY: 0.393 AC XY: 29238 AN XY: 74396

African (AFR) AF: 0.276 AC: 11465 AN: 41504

American (AMR) AF: 0.317 AC: 4853 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.424 AC: 1469 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1222 AN: 5172

South Asian (SAS) AF: 0.407 AC: 1963 AN: 4824

European-Finnish (FIN) AF: 0.449 AC: 4758 AN: 10594

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33420 AN: 67980

Other (OTH) AF: 0.382 AC: 807 AN: 2112

Alfa AF: 0.452 Hom.: 50557

Bravo AF: 0.381

Asia WGS AF: 0.327 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.72
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs11153730; hg19: chr6-118667522; COSMIC: COSV69422111;