ENST00000429636.1:n.196+116973A>T

Variant names:

• chr2-164133747-T-A
• rs12473215
• ENST00000429636.1:n.196+116973A>T

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.196+116973A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,208 control chromosomes in the GnomAD database, including 1,994 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 0.14 (1994 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.343

Genes affected

ENSG00000237844 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.248 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
ENSG00000237844	ENST00000429636.1	n.196+116973A>T		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.143 AC: 21683 AN: 152090 Hom.: 1993 Cov.: 32

Gnomad AFR AF: 0.0580

Gnomad AMI AF: 0.175

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0688

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.143 AC: 21695 AN: 152208 Hom.: 1994 Cov.: 32 AF XY: 0.146 AC XY: 10837 AN XY: 74402

Gnomad4 AFR AF: 0.0579

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0688

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.151

Alfa AF: 0.154 Hom.: 245

Bravo AF: 0.145

Asia WGS AF: 0.146 AC: 511 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	7.0
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12473215; hg19: chr2-164990257;