ENST00000843329.1:n.212+10576G>C

Variant names:

• chr8-10468602-C-G
• rs6995374
• ENST00000843329.1:n.212+10576G>C

Variant summary

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

The ENST00000843329.1(ENSG00000253678):​n.212+10576G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.223 in 151,030 control chromosomes in the GnomAD database, including 3,829 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 0.22 (3829 hom., cov: 30)
• Consequence: ENSG00000253678 ENST00000843329.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433
• Publications: 4 publications found

Genes affected

ENSG00000253678 (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 (AMR) allele frequency at 95% confidence interval = 0.26 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000843329.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253678	ENST00000843329.1		n.212+10576G>C		intron	N/A
	ENSG00000253678	ENST00000843330.1		n.213-2430G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33670 AN: 150910 Hom.: 3817 Cov.: 30

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.201

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.202

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

GnomAD4 genome AF: 0.223 AC: 33698 AN: 151030 Hom.: 3829 Cov.: 30 AF XY: 0.223 AC XY: 16473 AN XY: 73798

African (AFR) AF: 0.193 AC: 7922 AN: 41074

American (AMR) AF: 0.266 AC: 4043 AN: 15172

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 653 AN: 3466

East Asian (EAS) AF: 0.245 AC: 1251 AN: 5100

South Asian (SAS) AF: 0.185 AC: 882 AN: 4778

European-Finnish (FIN) AF: 0.198 AC: 2069 AN: 10430

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16211 AN: 67726

Other (OTH) AF: 0.212 AC: 442 AN: 2088

Alfa AF: 0.216 Hom.: 447

Bravo AF: 0.227

Asia WGS AF: 0.210 AC: 733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.4
DANN	Benign	0.59
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6995374; hg19: chr8-10326112;