8-100801040-G-T

Variant names:

• chr8-100801040-G-T
• rs3843552
• ENST00000822257.1:n.235+4224G>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+4224G>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 151,674 control chromosomes in the GnomAD database, including 1,894 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 (1894 hom., cov: 31)
• Consequence: ENSG00000306968 ENST00000822257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 4 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.

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+4224G>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19562 AN: 151556 Hom.: 1882 Cov.: 31

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0624

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.0806

Gnomad FIN AF: 0.0565

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0565

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: 19623 AN: 151674 Hom.: 1894 Cov.: 31 AF XY: 0.133 AC XY: 9830 AN XY: 74114

African (AFR) AF: 0.233 AC: 9597 AN: 41270

American (AMR) AF: 0.200 AC: 3047 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0624 AC: 216 AN: 3462

East Asian (EAS) AF: 0.315 AC: 1627 AN: 5160

South Asian (SAS) AF: 0.0811 AC: 388 AN: 4784

European-Finnish (FIN) AF: 0.0565 AC: 595 AN: 10530

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

European-Non Finnish (NFE) AF: 0.0564 AC: 3835 AN: 67950

Other (OTH) AF: 0.123 AC: 259 AN: 2104

Alfa AF: 0.0621 Hom.: 243

Bravo AF: 0.148

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.13
DANN	Benign	0.52
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs3843552; hg19: chr8-101813268;