rs11779303

Variant names:

• chr8-6208094-G-C
• rs11779303
• ENST00000519555.1:n.126+49318C>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000519555.1(ENSG00000253880):​n.126+49318C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,066 control chromosomes in the GnomAD database, including 1,982 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 0.15 (1982 hom., cov: 32)
• Consequence: ENSG00000253880 ENST00000519555.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150

Genes affected

ENSG00000253880 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 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
ENSG00000253880	ENST00000519555.1	n.126+49318C>G		intron_variant	Intron 1 of 4	4

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23354 AN: 151948 Hom.: 1974 Cov.: 32

Gnomad AFR AF: 0.0900

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0528

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.154 AC: 23390 AN: 152066 Hom.: 1982 Cov.: 32 AF XY: 0.151 AC XY: 11258 AN XY: 74334

Gnomad4 AFR AF: 0.0902

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0527

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.186

Alfa AF: 0.165 Hom.: 252

Bravo AF: 0.150

Asia WGS AF: 0.160 AC: 554 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.42
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11779303; hg19: chr8-6065615;