chr2-183911971-C-T

Variant names:

• chr2-183911971-C-T
• rs9333286
• ENST00000441026.1:n.103+7340C>T

Variant summary

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

The ENST00000441026.1(ENSG00000234172):​n.103+7340C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 151,928 control chromosomes in the GnomAD database, including 9,023 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 0.33 (9023 hom., cov: 33)
• Consequence: ENSG00000234172 ENST00000441026.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 0 publications found

Genes affected

ENSG00000234172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.569 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
ENSG00000234172	ENST00000441026.1	n.103+7340C>T		intron_variant	Intron 1 of 2	2
ENSG00000234172	ENST00000828168.1	n.139+7340C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50597 AN: 151810 Hom.: 9027 Cov.: 33

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.365

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.587

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.333 AC: 50616 AN: 151928 Hom.: 9023 Cov.: 33 AF XY: 0.330 AC XY: 24487 AN XY: 74278

African (AFR) AF: 0.215 AC: 8931 AN: 41460

American (AMR) AF: 0.345 AC: 5271 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.364 AC: 1263 AN: 3468

East Asian (EAS) AF: 0.586 AC: 3031 AN: 5168

South Asian (SAS) AF: 0.303 AC: 1462 AN: 4818

European-Finnish (FIN) AF: 0.335 AC: 3532 AN: 10542

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.384 AC: 26044 AN: 67902

Other (OTH) AF: 0.315 AC: 665 AN: 2108

Alfa AF: 0.352 Hom.: 1263

Bravo AF: 0.333

Asia WGS AF: 0.416 AC: 1434 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.2
DANN	Benign	0.47
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs9333286; hg19: chr2-184776698;