8-21230272-A-G

Variant names:

• chr8-21230272-A-G
• rs989329
• ENST00000657734.1:n.1326+64862T>C

Variant summary

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

The ENST00000657734.1(ENSG00000254092):​n.1326+64862T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.416 in 151,912 control chromosomes in the GnomAD database, including 17,178 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 0.42 (17178 hom., cov: 31)
• Consequence: ENSG00000254092 ENST00000657734.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293
• Publications: 2 publications found

Genes affected

ENSG00000254092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657734.1. 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
	ENSG00000254092	ENST00000657734.1		n.1326+64862T>C		intron	N/A
	ENSG00000254092	ENST00000659453.1		n.1639+64862T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.416 AC: 63157 AN: 151794 Hom.: 17130 Cov.: 31

Gnomad AFR AF: 0.774

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.276

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.416 AC: 63248 AN: 151912 Hom.: 17178 Cov.: 31 AF XY: 0.409 AC XY: 30402 AN XY: 74264

African (AFR) AF: 0.774 AC: 32071 AN: 41434

American (AMR) AF: 0.310 AC: 4728 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3470

East Asian (EAS) AF: 0.175 AC: 901 AN: 5136

South Asian (SAS) AF: 0.434 AC: 2076 AN: 4784

European-Finnish (FIN) AF: 0.203 AC: 2147 AN: 10568

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.276 AC: 18774 AN: 67942

Other (OTH) AF: 0.411 AC: 869 AN: 2116

Alfa AF: 0.330 Hom.: 31025

Bravo AF: 0.441

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.53
DANN	Benign	0.57
PhyloP100		-0.29

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: rs989329;

hg19: chr8-21087783;