ENST00000429636.1:n.196+143744A>G

Variant names:

• chr2-164106976-T-C
• rs1446468
• ENST00000429636.1:n.196+143744A>G

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.196+143744A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,988 control chromosomes in the GnomAD database, including 15,346 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 0.41 (15346 hom., cov: 31)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630

Genes affected

ENSG00000237844 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.535 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+143744A>G		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61779 AN: 151870 Hom.: 15351 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.406 AC: 61772 AN: 151988 Hom.: 15346 Cov.: 31 AF XY: 0.412 AC XY: 30585 AN XY: 74280

Gnomad4 AFR AF: 0.119

Gnomad4 AMR AF: 0.392

Gnomad4 ASJ AF: 0.454

Gnomad4 EAS AF: 0.537

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.622

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.399

Alfa AF: 0.503 Hom.: 7993

Bravo AF: 0.374

Asia WGS AF: 0.480 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1446468; hg19: chr2-164963486;