chr8-21381562-A-T

Variant names:

• chr8-21381562-A-T
• rs4382469
• ENST00000808781.1:n.318-15866T>A

Variant summary

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

The ENST00000808781.1(ENSG00000305102):​n.318-15866T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 152,118 control chromosomes in the GnomAD database, including 21,447 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 0.52 (21447 hom., cov: 33)
• Consequence: ENSG00000305102 ENST00000808781.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.28
• Publications: 1 publications found

Genes affected

ENSG00000305102 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808781.1. 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
	ENSG00000305102	ENST00000808781.1		n.318-15866T>A		intron	N/A
	ENSG00000305102	ENST00000808782.1		n.108-15866T>A		intron	N/A
	ENSG00000305102	ENST00000808783.1		n.133+6735T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.521 AC: 79176 AN: 152000 Hom.: 21425 Cov.: 33

Gnomad AFR AF: 0.381

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.461

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.521 AC: 79247 AN: 152118 Hom.: 21447 Cov.: 33 AF XY: 0.517 AC XY: 38474 AN XY: 74362

African (AFR) AF: 0.382 AC: 15844 AN: 41510

American (AMR) AF: 0.566 AC: 8658 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2324 AN: 3472

East Asian (EAS) AF: 0.538 AC: 2772 AN: 5154

South Asian (SAS) AF: 0.462 AC: 2224 AN: 4818

European-Finnish (FIN) AF: 0.538 AC: 5686 AN: 10578

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.588 AC: 39958 AN: 67988

Other (OTH) AF: 0.557 AC: 1173 AN: 2106

Alfa AF: 0.406 Hom.: 1122

Bravo AF: 0.518

Asia WGS AF: 0.471 AC: 1640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.012
DANN	Benign	0.80
PhyloP100		-2.3

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: rs4382469;

hg19: chr8-21239073;