chr20-46769636-T-C

Variant names:

• chr20-46769636-T-C
• rs3091430
• ENST00000840791.1:n.351-3812A>G

Variant summary

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

The ENST00000840791.1(ENSG00000309405):​n.351-3812A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 152,186 control chromosomes in the GnomAD database, including 7,972 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 0.29 (7972 hom., cov: 32)
• Consequence: ENSG00000309405 ENST00000840791.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591
• Publications: 1 publications found

Genes affected

ENSG00000309405 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.714 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840791.1. 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
	ENSG00000309405	ENST00000840791.1		n.351-3812A>G		intron	N/A
	ENSG00000309405	ENST00000840792.1		n.37-3812A>G		intron	N/A
	ENSG00000309405	ENST00000840793.1		n.169+1587A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43416 AN: 152068 Hom.: 7957 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.733

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.286 AC: 43453 AN: 152186 Hom.: 7972 Cov.: 32 AF XY: 0.299 AC XY: 22257 AN XY: 74404

African (AFR) AF: 0.108 AC: 4482 AN: 41558

American (AMR) AF: 0.442 AC: 6757 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1271 AN: 3472

East Asian (EAS) AF: 0.733 AC: 3796 AN: 5178

South Asian (SAS) AF: 0.572 AC: 2757 AN: 4822

European-Finnish (FIN) AF: 0.336 AC: 3558 AN: 10582

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19789 AN: 67976

Other (OTH) AF: 0.333 AC: 704 AN: 2112

Alfa AF: 0.283 Hom.: 855

Bravo AF: 0.285

Asia WGS AF: 0.620 AC: 2154 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.27
DANN	Benign	0.38
PhyloP100		-0.59

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: rs3091430;

hg19: chr20-45398275;