rs3847154

Variant names:

• chr8-100800950-C-T
• rs3847154
• ENST00000822257.1:n.235+4134C>T

Variant summary

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

The ENST00000822257.1(ENSG00000306968):​n.235+4134C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 151,692 control chromosomes in the GnomAD database, including 1,898 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 0.13 (1898 hom., cov: 31)
• Consequence: ENSG00000306968 ENST00000822257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.108
• Publications: 3 publications found

Genes affected

ENSG00000306968 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 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
ENSG00000306968	ENST00000822257.1	n.235+4134C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19567 AN: 151574 Hom.: 1886 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0496

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0623

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0813

Gnomad FIN AF: 0.0563

Gnomad MID AF: 0.0382

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.123

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

GnomAD4 genome AF: 0.129 AC: 19628 AN: 151692 Hom.: 1898 Cov.: 31 AF XY: 0.133 AC XY: 9835 AN XY: 74138

African (AFR) AF: 0.233 AC: 9599 AN: 41278

American (AMR) AF: 0.201 AC: 3051 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.0623 AC: 216 AN: 3468

East Asian (EAS) AF: 0.316 AC: 1629 AN: 5160

South Asian (SAS) AF: 0.0817 AC: 392 AN: 4796

European-Finnish (FIN) AF: 0.0563 AC: 594 AN: 10544

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0564 AC: 3830 AN: 67946

Other (OTH) AF: 0.123 AC: 259 AN: 2102

Alfa AF: 0.106 Hom.: 211

Bravo AF: 0.148

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.74
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs3847154; hg19: chr8-101813178;