2-19429543-T-C

Variant names:

• chr2-19429543-T-C
• rs13398721
• ENST00000811606.1:n.177+20468A>G

Variant summary

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

The ENST00000811606.1(ENSG00000305536):​n.177+20468A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,200 control chromosomes in the GnomAD database, including 4,854 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 0.22 (4854 hom., cov: 33)
• Consequence: ENSG00000305536 ENST00000811606.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.496
• Publications: 5 publications found

Genes affected

ENSG00000305536 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.759 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
ENSG00000305536	ENST00000811606.1	n.177+20468A>G		intron_variant	Intron 1 of 2
ENSG00000305536	ENST00000811607.1	n.177+10911A>G		intron_variant	Intron 1 of 2
ENSG00000305536	ENST00000811608.1	n.40+10911A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.217 AC: 33034 AN: 152082 Hom.: 4851 Cov.: 33

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.779

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.217 AC: 33052 AN: 152200 Hom.: 4854 Cov.: 33 AF XY: 0.222 AC XY: 16520 AN XY: 74418

African (AFR) AF: 0.277 AC: 11490 AN: 41506

American (AMR) AF: 0.286 AC: 4374 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 431 AN: 3472

East Asian (EAS) AF: 0.779 AC: 4034 AN: 5178

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4824

European-Finnish (FIN) AF: 0.135 AC: 1427 AN: 10600

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9477 AN: 68002

Other (OTH) AF: 0.239 AC: 505 AN: 2116

Alfa AF: 0.174 Hom.: 8727

Bravo AF: 0.238

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	9.2
DANN	Benign	0.88
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs13398721; hg19: chr2-19629304;