rs3843776

Variant names:

• chr20-24009015-G-A
• rs3843776
• ENST00000846737.1:n.228+12442G>A

Variant summary

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

The ENST00000846737.1(ENSG00000310043):​n.228+12442G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 152,098 control chromosomes in the GnomAD database, including 8,686 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 0.23 (8686 hom., cov: 33)
• Consequence: ENSG00000310043 ENST00000846737.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 3 publications found

Genes affected

ENSG00000310043 (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 (AFR) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310043	ENST00000846737.1	n.228+12442G>A		intron_variant	Intron 2 of 3
ENSG00000310043	ENST00000846738.1	n.513-4580G>A		intron_variant	Intron 2 of 2
ENSG00000310054	ENST00000846818.1	n.125+95C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35437 AN: 151980 Hom.: 8640 Cov.: 33

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0799

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0641

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.234 AC: 35543 AN: 152098 Hom.: 8686 Cov.: 33 AF XY: 0.234 AC XY: 17394 AN XY: 74356

African (AFR) AF: 0.620 AC: 25671 AN: 41426

American (AMR) AF: 0.0970 AC: 1484 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 463 AN: 3472

East Asian (EAS) AF: 0.0795 AC: 412 AN: 5182

South Asian (SAS) AF: 0.182 AC: 880 AN: 4826

European-Finnish (FIN) AF: 0.159 AC: 1685 AN: 10574

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.0641 AC: 4358 AN: 68004

Other (OTH) AF: 0.180 AC: 381 AN: 2114

Alfa AF: 0.140 Hom.: 1502

Bravo AF: 0.244

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.79
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs3843776; hg19: chr20-23989652;