2-163762315-G-A

Variant names:

• chr2-163762315-G-A
• rs10189532
• ENST00000429636.1:n.380-12408C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000429636.1(ENSG00000237844):​n.380-12408C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 151,918 control chromosomes in the GnomAD database, including 1,766 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 (1766 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193
• Publications: 2 publications found

Genes affected

ENSG00000237844 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 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.380-12408C>T		intron_variant	Intron 4 of 4	3
ENSG00000237844	ENST00000666867.1	n.455-12408C>T		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21357 AN: 151800 Hom.: 1761 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0551

Gnomad EAS AF: 0.0126

Gnomad SAS AF: 0.112

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.141 AC: 21385 AN: 151918 Hom.: 1766 Cov.: 32 AF XY: 0.139 AC XY: 10351 AN XY: 74282

African (AFR) AF: 0.229 AC: 9484 AN: 41422

American (AMR) AF: 0.115 AC: 1752 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0551 AC: 191 AN: 3468

East Asian (EAS) AF: 0.0126 AC: 65 AN: 5152

South Asian (SAS) AF: 0.111 AC: 533 AN: 4818

European-Finnish (FIN) AF: 0.109 AC: 1154 AN: 10582

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.115 AC: 7781 AN: 67922

Other (OTH) AF: 0.129 AC: 273 AN: 2112

Alfa AF: 0.132 Hom.: 1125

Bravo AF: 0.143

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	14
DANN	Benign	0.57
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10189532; hg19: chr2-164618825;