8-34004551-G-A

Variant names:

• chr8-34004551-G-A
• rs7823476
• ENST00000518163.6:n.228+4971C>T

Variant summary

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

The ENST00000521541.2(ENSG00000253642):​n.314-3305G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.645 in 152,138 control chromosomes in the GnomAD database, including 34,951 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 0.65 (34951 hom., cov: 33)
• Consequence: ENSG00000253642 ENST00000521541.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.319
• Publications: 0 publications found

Genes affected

ENSG00000254194 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000521541.2. 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
	LOC105379364	NR_189605.1		n.746-30335G>A		intron	N/A
	LOC105379364	NR_189606.1		n.331-3305G>A		intron	N/A
	LOC105379364	NR_189607.1		n.331-129038G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254194	ENST00000518163.6	TSL:3	n.228+4971C>T		intron	N/A
	ENSG00000253642	ENST00000521541.2	TSL:2	n.314-3305G>A		intron	N/A
	ENSG00000254194	ENST00000521714.1	TSL:2	n.171+689C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98185 AN: 152020 Hom.: 34951 Cov.: 33

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.649

Gnomad AMR AF: 0.726

Gnomad ASJ AF: 0.846

Gnomad EAS AF: 0.681

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.645 AC: 98194 AN: 152138 Hom.: 34951 Cov.: 33 AF XY: 0.651 AC XY: 48436 AN XY: 74372

African (AFR) AF: 0.316 AC: 13120 AN: 41502

American (AMR) AF: 0.726 AC: 11111 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.846 AC: 2935 AN: 3470

East Asian (EAS) AF: 0.681 AC: 3511 AN: 5154

South Asian (SAS) AF: 0.789 AC: 3805 AN: 4822

European-Finnish (FIN) AF: 0.792 AC: 8381 AN: 10582

Middle Eastern (MID) AF: 0.789 AC: 232 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53062 AN: 67992

Other (OTH) AF: 0.684 AC: 1445 AN: 2114

Alfa AF: 0.589 Hom.: 2105

Bravo AF: 0.629

Asia WGS AF: 0.715 AC: 2488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	3.6
DANN	Benign	0.84
PhyloP100		0.32

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7823476;

hg19: chr8-33862069;