ENST00000518163.6:n.228+3513G>C

Variant names:

• chr8-34006009-C-G
• rs7463344
• ENST00000518163.6:n.228+3513G>C

Variant summary

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

The ENST00000518163.6(ENSG00000254194):​n.228+3513G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.872 in 151,970 control chromosomes in the GnomAD database, including 60,633 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 0.87 (60633 hom., cov: 29)
• Consequence: ENSG00000254194 ENST00000518163.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.364
• Publications: 4 publications found

Genes affected

ENSG00000254194 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379364	NR_189605.1	n.746-28877C>G		intron_variant	Intron 3 of 11
LOC105379364	NR_189606.1	n.331-1847C>G		intron_variant	Intron 2 of 9
LOC105379364	NR_189607.1	n.331-127580C>G		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254194	ENST00000518163.6	n.228+3513G>C		intron_variant	Intron 3 of 4	3
ENSG00000253642	ENST00000521541.2	n.314-1847C>G		intron_variant	Intron 2 of 3	2
ENSG00000254194	ENST00000521714.1	n.75-673G>C		intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132533 AN: 151852 Hom.: 60620 Cov.: 29

Gnomad AFR AF: 0.564

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.948

Gnomad ASJ AF: 0.988

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.995

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.903

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

GnomAD4 genome AF: 0.872 AC: 132575 AN: 151970 Hom.: 60633 Cov.: 29 AF XY: 0.876 AC XY: 65102 AN XY: 74280

African (AFR) AF: 0.564 AC: 23305 AN: 41348

American (AMR) AF: 0.948 AC: 14483 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.988 AC: 3428 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5130 AN: 5132

South Asian (SAS) AF: 0.995 AC: 4798 AN: 4820

European-Finnish (FIN) AF: 1.00 AC: 10598 AN: 10600

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.996 AC: 67742 AN: 68016

Other (OTH) AF: 0.904 AC: 1906 AN: 2108

Alfa AF: 0.920 Hom.: 3438

Bravo AF: 0.855

Asia WGS AF: 0.972 AC: 3380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.6
DANN	Benign	0.60
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs7463344; hg19: chr8-33863527;