ENST00000518163.6:n.229-3972T>G

Variant names:

• chr8-33979515-A-C
• rs7463110
• ENST00000518163.6:n.229-3972T>G

Variant summary

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

The ENST00000518163.6(ENSG00000254194):​n.229-3972T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 151,924 control chromosomes in the GnomAD database, including 22,024 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 0.53 (22024 hom., cov: 32)
• Consequence: ENSG00000254194 ENST00000518163.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379364	NR_189605.1	n.746-55371A>C		intron_variant	Intron 3 of 11
LOC105379364	NR_189606.1	n.331-28341A>C		intron_variant	Intron 2 of 9
LOC105379364	NR_189607.1	n.331-154074A>C		intron_variant	Intron 2 of 8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000254194	ENST00000518163.6	n.229-3972T>G		intron_variant	Intron 3 of 4	3
ENSG00000253642	ENST00000521541.2	n.314-28341A>C		intron_variant	Intron 2 of 3	2
ENSG00000254194	ENST00000521714.1	n.172-3972T>G		intron_variant	Intron 2 of 3	2

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81108 AN: 151806 Hom.: 22011 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.552

Gnomad AMR AF: 0.547

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.825

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.534 AC: 81153 AN: 151924 Hom.: 22024 Cov.: 32 AF XY: 0.536 AC XY: 39772 AN XY: 74268

African (AFR) AF: 0.501 AC: 20738 AN: 41404

American (AMR) AF: 0.547 AC: 8356 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1380 AN: 3466

East Asian (EAS) AF: 0.825 AC: 4264 AN: 5166

South Asian (SAS) AF: 0.686 AC: 3306 AN: 4822

European-Finnish (FIN) AF: 0.512 AC: 5391 AN: 10532

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36046 AN: 67932

Other (OTH) AF: 0.501 AC: 1056 AN: 2108

Alfa AF: 0.513 Hom.: 4926

Bravo AF: 0.532

Asia WGS AF: 0.723 AC: 2511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.0
DANN	Benign	0.57
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs7463110; hg19: chr8-33837033;