2-231599597-T-C

Variant names:

• chr2-231599597-T-C
• rs13384421
• ENST00000778821.1:n.410+4152A>G

Variant summary

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

The ENST00000778821.1(ENSG00000286399):​n.410+4152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,950 control chromosomes in the GnomAD database, including 13,096 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 0.40 (13096 hom., cov: 32)
• Consequence: ENSG00000286399 ENST00000778821.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.226
• Publications: 4 publications found

Genes affected

ENSG00000286399 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000778821.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286399	ENST00000778821.1		n.410+4152A>G		intron	N/A
	ENSG00000286399	ENST00000778822.1		n.336+4152A>G		intron	N/A
	ENSG00000286399	ENST00000778823.1		n.245+4282A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60648 AN: 151832 Hom.: 13091 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.536

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.447

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.399 AC: 60659 AN: 151950 Hom.: 13096 Cov.: 32 AF XY: 0.397 AC XY: 29472 AN XY: 74242

African (AFR) AF: 0.231 AC: 9576 AN: 41478

American (AMR) AF: 0.405 AC: 6191 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3468

East Asian (EAS) AF: 0.446 AC: 2298 AN: 5150

South Asian (SAS) AF: 0.346 AC: 1666 AN: 4812

European-Finnish (FIN) AF: 0.471 AC: 4957 AN: 10528

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33211 AN: 67934

Other (OTH) AF: 0.369 AC: 778 AN: 2106

Alfa AF: 0.454 Hom.: 27524

Bravo AF: 0.388

Asia WGS AF: 0.350 AC: 1216 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.3
DANN	Benign	0.68
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs13384421; hg19: chr2-232464308;