8-100798263-T-C

Variant names:

• chr8-100798263-T-C
• rs10808365
• ENST00000822257.1:n.235+1447T>C

Variant summary

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

The ENST00000822257.1(ENSG00000306968):​n.235+1447T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,158 control chromosomes in the GnomAD database, including 1,901 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 (1901 hom., cov: 32)
• Consequence: ENSG00000306968 ENST00000822257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.514
• Publications: 2 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.302 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+1447T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19656 AN: 152040 Hom.: 1889 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0622

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.0832

Gnomad FIN AF: 0.0566

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: 0.130 AC: 19716 AN: 152158 Hom.: 1901 Cov.: 32 AF XY: 0.133 AC XY: 9881 AN XY: 74396

African (AFR) AF: 0.233 AC: 9644 AN: 41478

American (AMR) AF: 0.201 AC: 3062 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0622 AC: 216 AN: 3470

East Asian (EAS) AF: 0.315 AC: 1630 AN: 5172

South Asian (SAS) AF: 0.0837 AC: 404 AN: 4826

European-Finnish (FIN) AF: 0.0566 AC: 601 AN: 10610

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

European-Non Finnish (NFE) AF: 0.0564 AC: 3839 AN: 68014

Other (OTH) AF: 0.123 AC: 261 AN: 2114

Alfa AF: 0.106 Hom.: 211

Bravo AF: 0.148

Asia WGS AF: 0.182 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.5
DANN	Benign	0.50
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs10808365; hg19: chr8-101810491;