8-100803005-T-C

Variant names:

• chr8-100803005-T-C
• rs3843555
• ENST00000822257.1:n.235+6189T>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+6189T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,076 control chromosomes in the GnomAD database, including 1,412 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 0.11 (1412 hom., cov: 31)
• Consequence: ENSG00000306968 ENST00000822257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.473
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.305 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+6189T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17388 AN: 151958 Hom.: 1404 Cov.: 31

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.0649

Gnomad EAS AF: 0.317

Gnomad SAS AF: 0.0905

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0566

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.115 AC: 17443 AN: 152076 Hom.: 1412 Cov.: 31 AF XY: 0.118 AC XY: 8800 AN XY: 74334

African (AFR) AF: 0.177 AC: 7332 AN: 41470

American (AMR) AF: 0.199 AC: 3040 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0649 AC: 225 AN: 3466

East Asian (EAS) AF: 0.318 AC: 1641 AN: 5164

South Asian (SAS) AF: 0.0910 AC: 439 AN: 4824

European-Finnish (FIN) AF: 0.0579 AC: 613 AN: 10592

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0566 AC: 3849 AN: 67980

Other (OTH) AF: 0.118 AC: 250 AN: 2114

Alfa AF: 0.0604 Hom.: 97

Bravo AF: 0.130

Asia WGS AF: 0.188 AC: 652 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.46
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs3843555; hg19: chr8-101815233;