8-100800846-C-T

Variant names:

• chr8-100800846-C-T
• rs3847152
• ENST00000822257.1:n.235+4030C>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+4030C>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 150,866 control chromosomes in the GnomAD database, including 1,884 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 (1884 hom., cov: 30)
• Consequence: ENSG00000306968 ENST00000822257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00500
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.303 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000822257.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306968	ENST00000822257.1		n.235+4030C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19390 AN: 150748 Hom.: 1872 Cov.: 30

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0507

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0621

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0809

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0564

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.129 AC: 19452 AN: 150866 Hom.: 1884 Cov.: 30 AF XY: 0.132 AC XY: 9716 AN XY: 73578

African (AFR) AF: 0.232 AC: 9508 AN: 40952

American (AMR) AF: 0.200 AC: 2998 AN: 15020

Ashkenazi Jewish (ASJ) AF: 0.0621 AC: 215 AN: 3460

East Asian (EAS) AF: 0.316 AC: 1625 AN: 5144

South Asian (SAS) AF: 0.0814 AC: 385 AN: 4732

European-Finnish (FIN) AF: 0.0560 AC: 583 AN: 10406

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0563 AC: 3824 AN: 67862

Other (OTH) AF: 0.122 AC: 255 AN: 2088

Alfa AF: 0.106 Hom.: 212

Bravo AF: 0.148

Asia WGS AF: 0.180 AC: 625 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	3.2
DANN	Benign	0.47
PhyloP100		0.0050

Splicing

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

Other links and lift over

dbSNP: rs3847152; hg19: chr8-101813074;