rs13404596

Variant names:

• chr2-200907078-T-G
• rs13404596
• ENST00000831870.1:n.222-2765A>C

Variant summary

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

The ENST00000831870.1(ENSG00000308129):​n.222-2765A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 146,912 control chromosomes in the GnomAD database, including 4,608 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 (4608 hom., cov: 30)
• Consequence: ENSG00000308129 ENST00000831870.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.348
• Publications: 8 publications found

Genes affected

ENSG00000308129 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.378 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
ENSG00000308129	ENST00000831870.1	n.222-2765A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.234 AC: 34309 AN: 146778 Hom.: 4600 Cov.: 30

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.175

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.00956

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.174

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.230

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

GnomAD4 genome AF: 0.234 AC: 34359 AN: 146912 Hom.: 4608 Cov.: 30 AF XY: 0.229 AC XY: 16447 AN XY: 71718

African (AFR) AF: 0.383 AC: 15394 AN: 40218

American (AMR) AF: 0.175 AC: 2576 AN: 14762

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 826 AN: 3400

East Asian (EAS) AF: 0.00959 AC: 44 AN: 4590

South Asian (SAS) AF: 0.0848 AC: 387 AN: 4562

European-Finnish (FIN) AF: 0.186 AC: 1883 AN: 10102

Middle Eastern (MID) AF: 0.168 AC: 38 AN: 226

European-Non Finnish (NFE) AF: 0.190 AC: 12589 AN: 66170

Other (OTH) AF: 0.227 AC: 459 AN: 2022

Alfa AF: 0.217 Hom.: 523

Bravo AF: 0.236

Asia WGS AF: 0.0730 AC: 256 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.1
DANN	Benign	0.72
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs13404596; hg19: chr2-201771801;