ENST00000655387.2:n.435-35241G>A

Variant names:

• chr3-39328191-C-T
• rs12107527
• ENST00000655387.2:n.435-35241G>A

Variant summary

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

The ENST00000655387.2(ENSG00000287780):​n.435-35241G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 152,118 control chromosomes in the GnomAD database, including 4,997 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 0.24 (4997 hom., cov: 32)
• Consequence: ENSG00000287780 ENST00000655387.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 10 publications found

Genes affected

ENSG00000287780 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655387.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287780	ENST00000655387.2		n.435-35241G>A		intron	N/A
	ENSG00000287780	ENST00000836879.1		n.288-35241G>A		intron	N/A
	ENSG00000287780	ENST00000836880.1		n.373-35241G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.243 AC: 37012 AN: 152000 Hom.: 4996 Cov.: 32

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.234

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.243 AC: 37032 AN: 152118 Hom.: 4997 Cov.: 32 AF XY: 0.235 AC XY: 17488 AN XY: 74370

African (AFR) AF: 0.199 AC: 8237 AN: 41492

American (AMR) AF: 0.191 AC: 2920 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.241 AC: 835 AN: 3468

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5180

South Asian (SAS) AF: 0.126 AC: 609 AN: 4822

European-Finnish (FIN) AF: 0.234 AC: 2482 AN: 10588

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.309 AC: 21010 AN: 67982

Other (OTH) AF: 0.254 AC: 537 AN: 2114

Alfa AF: 0.277 Hom.: 19815

Bravo AF: 0.238

Asia WGS AF: 0.0650 AC: 228 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.71
DANN	Benign	0.58
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12107527; hg19: chr3-39369682; COSMIC: COSV58337517;