ENST00000519555.1:n.126+49318C>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000253880 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519555.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253880	ENST00000519555.1	TSL:4	n.126+49318C>G		intron	N/A

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

African (AFR) AF: 0.0902 AC: 3740 AN: 41462

American (AMR) AF: 0.145 AC: 2218 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 800 AN: 3472

East Asian (EAS) AF: 0.0527 AC: 273 AN: 5180

South Asian (SAS) AF: 0.198 AC: 956 AN: 4818

European-Finnish (FIN) AF: 0.138 AC: 1460 AN: 10570

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.197 AC: 13403 AN: 67976

Other (OTH) AF: 0.186 AC: 391 AN: 2106

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.42
DANN	Benign	0.39
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs11779303; hg19: chr8-6065615;