2-164179377-A-T

Variant names:

• chr2-164179377-A-T
• rs1446466
• ENST00000429636.1:n.196+71343T>A

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.196+71343T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,238 control chromosomes in the GnomAD database, including 2,192 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 0.15 (2192 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20
• Publications: 3 publications found

Genes affected

ENSG00000237844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.256 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+71343T>A		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23504 AN: 152120 Hom.: 2190 Cov.: 32

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0397

Gnomad SAS AF: 0.252

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.155 AC: 23523 AN: 152238 Hom.: 2192 Cov.: 32 AF XY: 0.158 AC XY: 11739 AN XY: 74420

African (AFR) AF: 0.0913 AC: 3796 AN: 41562

American (AMR) AF: 0.262 AC: 4012 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 525 AN: 3472

East Asian (EAS) AF: 0.0396 AC: 205 AN: 5178

South Asian (SAS) AF: 0.253 AC: 1222 AN: 4824

European-Finnish (FIN) AF: 0.152 AC: 1608 AN: 10588

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11610 AN: 68008

Other (OTH) AF: 0.167 AC: 352 AN: 2112

Alfa AF: 0.0793 Hom.: 103

Bravo AF: 0.158

Asia WGS AF: 0.149 AC: 522 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	20
DANN	Benign	0.81
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs1446466; hg19: chr2-165035887;