chr8-11986249-G-A

Variant names:

• chr8-11986249-G-A
• rs4841662
• ENST00000715788.1:n.297+28582C>T

Variant summary

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

The ENST00000715788.1(ENSG00000290829):​n.297+28582C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,240 control chromosomes in the GnomAD database, including 17,845 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 0.45 (17845 hom., cov: 34)
• Consequence: ENSG00000290829 ENST00000715788.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 15 publications found

Genes affected

ENSG00000290829 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715788.1. 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
	ENSG00000290829	ENST00000715788.1		n.297+28582C>T		intron	N/A
	ENSG00000290829	ENST00000715789.1		n.333+28582C>T		intron	N/A
	ENSG00000290829	ENST00000715790.1		n.351+28582C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.446 AC: 67850 AN: 152120 Hom.: 17831 Cov.: 34

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.404

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.446 AC: 67900 AN: 152240 Hom.: 17845 Cov.: 34 AF XY: 0.462 AC XY: 34426 AN XY: 74438

African (AFR) AF: 0.184 AC: 7656 AN: 41544

American (AMR) AF: 0.612 AC: 9364 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.404 AC: 1401 AN: 3468

East Asian (EAS) AF: 0.911 AC: 4724 AN: 5186

South Asian (SAS) AF: 0.597 AC: 2882 AN: 4824

European-Finnish (FIN) AF: 0.637 AC: 6749 AN: 10596

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33388 AN: 68002

Other (OTH) AF: 0.474 AC: 1002 AN: 2112

Alfa AF: 0.480 Hom.: 77828

Bravo AF: 0.436

Asia WGS AF: 0.698 AC: 2424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.2
DANN	Benign	0.74
PhyloP100		0.35

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: rs4841662;

hg19: chr8-11843758;