rs113023

Variant names:

• chr22-39096758-C-T
• rs113023
• ENST00000815703.1:n.343G>A

Variant summary

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

The ENST00000815703.1(ENSG00000306155):​n.343G>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 0.46 in 151,592 control chromosomes in the GnomAD database, including 16,640 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 0.46 (16640 hom., cov: 29)
• Consequence: ENSG00000306155 ENST00000815703.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.375
• Publications: 4 publications found

Genes affected

ENSG00000306155 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.581 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
ENSG00000306155	ENST00000815703.1	n.343G>A		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.460 AC: 69711 AN: 151476 Hom.: 16634 Cov.: 29

Gnomad AFR AF: 0.587

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.372

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.484

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.460 AC: 69754 AN: 151592 Hom.: 16640 Cov.: 29 AF XY: 0.459 AC XY: 34018 AN XY: 74056

African (AFR) AF: 0.587 AC: 24245 AN: 41296

American (AMR) AF: 0.372 AC: 5652 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1520 AN: 3466

East Asian (EAS) AF: 0.293 AC: 1501 AN: 5128

South Asian (SAS) AF: 0.427 AC: 2055 AN: 4816

European-Finnish (FIN) AF: 0.484 AC: 5087 AN: 10520

Middle Eastern (MID) AF: 0.424 AC: 123 AN: 290

European-Non Finnish (NFE) AF: 0.416 AC: 28248 AN: 67876

Other (OTH) AF: 0.430 AC: 903 AN: 2098

Alfa AF: 0.448 Hom.: 1997

Bravo AF: 0.454

Asia WGS AF: 0.343 AC: 1196 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	5.0
DANN	Benign	0.37
PhyloP100		-0.38
PromoterAI		-0.029	Neutral

Splicing

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

Other links and lift over

dbSNP: rs113023; hg19: chr22-39492763;