2-164050310-C-T

Variant names:

• chr2-164050310-C-T
• rs16849225
• ENST00000429636.1:n.197-100051G>A

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.197-100051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,094 control chromosomes in the GnomAD database, including 3,439 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 0.20 (3439 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.745
• Publications: 33 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.372 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.197-100051G>A		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30303 AN: 151976 Hom.: 3436 Cov.: 32

Gnomad AFR AF: 0.102

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.386

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.212

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.235

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.199 AC: 30329 AN: 152094 Hom.: 3439 Cov.: 32 AF XY: 0.199 AC XY: 14833 AN XY: 74374

African (AFR) AF: 0.102 AC: 4235 AN: 41502

American (AMR) AF: 0.209 AC: 3200 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3468

East Asian (EAS) AF: 0.386 AC: 1994 AN: 5170

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4822

European-Finnish (FIN) AF: 0.212 AC: 2241 AN: 10576

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.235 AC: 15939 AN: 67960

Other (OTH) AF: 0.209 AC: 441 AN: 2108

Alfa AF: 0.220 Hom.: 8628

Bravo AF: 0.197

Asia WGS AF: 0.299 AC: 1038 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.50
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs16849225; hg19: chr2-164906820;