chr8-38469769-A-G

Variant names:

• chr8-38469769-A-G
• rs7825208
• ENST00000812829.1:n.66+3208A>G

Variant summary

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

The ENST00000812829.1(ENSG00000305763):​n.66+3208A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,202 control chromosomes in the GnomAD database, including 2,142 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 0.16 (2142 hom., cov: 32)
• Consequence: ENSG00000305763 ENST00000812829.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.182
• Publications: 13 publications found

Genes affected

ENSG00000305763 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.236 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812829.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000305763	ENST00000812829.1		n.66+3208A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24423 AN: 152084 Hom.: 2140 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.0461

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.209

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.161 AC: 24429 AN: 152202 Hom.: 2142 Cov.: 32 AF XY: 0.160 AC XY: 11894 AN XY: 74418

African (AFR) AF: 0.240 AC: 9942 AN: 41494

American (AMR) AF: 0.150 AC: 2296 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 500 AN: 3468

East Asian (EAS) AF: 0.163 AC: 846 AN: 5178

South Asian (SAS) AF: 0.207 AC: 1000 AN: 4828

European-Finnish (FIN) AF: 0.109 AC: 1152 AN: 10606

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8302 AN: 68010

Other (OTH) AF: 0.152 AC: 322 AN: 2114

Alfa AF: 0.136 Hom.: 5745

Bravo AF: 0.162

Asia WGS AF: 0.184 AC: 638 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.4
DANN	Benign	0.60
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs7825208; hg19: chr8-38327287;