rs2739330

Variant names:

• chr22-23953099-T-C
• rs2739330
• ENST00000440099.1:n.134-788T>C

Your query was ambiguous. Multiple possible variants found:

• chr22-23953099-T-C
• chr22-23953099-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000703580.1(ENSG00000290199):​n.309+20669A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 147,752 control chromosomes in the GnomAD database, including 23,139 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 0.58 (23139 hom., cov: 44)
• Consequence: ENSG00000290199 ENST00000703580.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00600

Genes affected

ENSG00000231271 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.672 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
ENSG00000231271	ENST00000440099.1	n.134-788T>C		intron_variant	Intron 2 of 2	6
ENSG00000290199	ENST00000703580.1	n.309+20669A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.576 AC: 85049 AN: 147638 Hom.: 23116 Cov.: 44

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.748

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.555

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.635

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.602

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.576 AC: 85113 AN: 147752 Hom.: 23139 Cov.: 44 AF XY: 0.581 AC XY: 41902 AN XY: 72124

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.603

Gnomad4 ASJ AF: 0.555

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.692

Gnomad4 FIN AF: 0.635

Gnomad4 NFE AF: 0.602

Gnomad4 OTH AF: 0.578

Alfa AF: 0.582 Hom.: 2751

Asia WGS AF: 0.505 AC: 1688 AN: 3346

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2739330; hg19: chr22-24295286;