rs7839244

Variant names:

• chr8-141378155-G-A
• rs7839244
• ENST00000835636.1:n.524G>A

Variant summary

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

The ENST00000835636.1(ENSG00000289263):​n.524G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,202 control chromosomes in the GnomAD database, including 3,699 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 0.19 (3699 hom., cov: 33)
• Consequence: ENSG00000289263 ENST00000835636.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.31
• Publications: 4 publications found

Genes affected

ENSG00000289263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.41 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000835636.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289263	ENST00000835636.1		n.524G>A		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000289263	ENST00000835640.1		n.309G>A		non_coding_transcript_exon	Exon 2 of 3
	ENSG00000289263	ENST00000835644.1		n.524G>A		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28380 AN: 152084 Hom.: 3689 Cov.: 33

Gnomad AFR AF: 0.330

Gnomad AMI AF: 0.142

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.0868

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0946

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.187 AC: 28432 AN: 152202 Hom.: 3699 Cov.: 33 AF XY: 0.188 AC XY: 14003 AN XY: 74420

African (AFR) AF: 0.331 AC: 13724 AN: 41498

American (AMR) AF: 0.216 AC: 3311 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 527 AN: 3468

East Asian (EAS) AF: 0.425 AC: 2198 AN: 5174

South Asian (SAS) AF: 0.171 AC: 823 AN: 4826

European-Finnish (FIN) AF: 0.0868 AC: 920 AN: 10598

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0946 AC: 6436 AN: 68020

Other (OTH) AF: 0.157 AC: 332 AN: 2114

Alfa AF: 0.122 Hom.: 900

Bravo AF: 0.206

Asia WGS AF: 0.274 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.033
DANN	Benign	0.53
PhyloP100		-3.3

Splicing

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

Other links and lift over

dbSNP: rs7839244; hg19: chr8-142388255;