rs3843777

Variant names:

• chr20-24009145-C-T
• rs3843777
• ENST00000846818.1:n.90G>A

Variant summary

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

The ENST00000846818.1(ENSG00000310054):​n.90G>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 0.234 in 152,170 control chromosomes in the GnomAD database, including 8,690 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 (8690 hom., cov: 33)
• Consequence: ENSG00000310054 ENST00000846818.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.961
• Publications: 2 publications found

Genes affected

ENSG00000310054 (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 (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
ENSG00000310054	ENST00000846818.1	n.90G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000310054	ENST00000846819.1	n.95G>A		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000310054	ENST00000846820.1	n.81G>A		non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35455 AN: 152052 Hom.: 8644 Cov.: 33

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.0973

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.0817

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.234 AC: 35561 AN: 152170 Hom.: 8690 Cov.: 33 AF XY: 0.234 AC XY: 17403 AN XY: 74390

African (AFR) AF: 0.619 AC: 25690 AN: 41488

American (AMR) AF: 0.0970 AC: 1484 AN: 15300

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

East Asian (EAS) AF: 0.0813 AC: 421 AN: 5176

South Asian (SAS) AF: 0.182 AC: 876 AN: 4820

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10584

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

European-Non Finnish (NFE) AF: 0.0640 AC: 4355 AN: 68016

Other (OTH) AF: 0.180 AC: 379 AN: 2110

Alfa AF: 0.182 Hom.: 816

Bravo AF: 0.245

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	-1.0
CADD	Benign	2.1
DANN	Benign	0.30
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs3843777; hg19: chr20-23989782;