rs730402

Variant names:

• chr2-59867571-G-A
• rs730402
• ENST00000606382.1:n.111-40300C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-59867571-G-A
• chr2-59867571-G-C

Variant summary

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

The ENST00000650011.1(ENSG00000233891):​n.274-9007C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.514 in 152,096 control chromosomes in the GnomAD database, including 20,670 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 0.51 (20670 hom., cov: 33)
• Consequence: ENSG00000233891 ENST00000650011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.106
• Publications: 9 publications found

Genes affected

ENSG00000233891 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650011.1. 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
	ENSG00000233891	ENST00000606382.1	TSL:5	n.111-40300C>T		intron	N/A
	ENSG00000233891	ENST00000650011.1		n.274-9007C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78133 AN: 151978 Hom.: 20637 Cov.: 33

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.506

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.514 AC: 78209 AN: 152096 Hom.: 20670 Cov.: 33 AF XY: 0.515 AC XY: 38284 AN XY: 74338

African (AFR) AF: 0.629 AC: 26089 AN: 41496

American (AMR) AF: 0.507 AC: 7736 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1585 AN: 3470

East Asian (EAS) AF: 0.409 AC: 2113 AN: 5162

South Asian (SAS) AF: 0.444 AC: 2142 AN: 4824

European-Finnish (FIN) AF: 0.511 AC: 5401 AN: 10574

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31595 AN: 67990

Other (OTH) AF: 0.486 AC: 1026 AN: 2112

Alfa AF: 0.473 Hom.: 29346

Bravo AF: 0.519

Asia WGS AF: 0.423 AC: 1470 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.9
DANN	Benign	0.63
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs730402; hg19: chr2-60094706;