2-200964879-C-G

Variant names:

• chr2-200964879-C-G
• rs874358
• ENST00000332935.6:n.332+1249C>G

Variant summary

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

The ENST00000332935.6(ENSG00000183308):​n.332+1249C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 152,074 control chromosomes in the GnomAD database, including 4,717 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 0.23 (4717 hom., cov: 32)
• Consequence: ENSG00000183308 ENST00000332935.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143
• Publications: 9 publications found

Genes affected

ENSG00000183308 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373835	NR_187975.1	n.199+1249C>G		intron_variant	Intron 1 of 2
LOC105373835	NR_187976.1	n.199+1249C>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000183308	ENST00000332935.6	n.332+1249C>G		intron_variant	Intron 1 of 1	3
ENSG00000183308	ENST00000413848.1	n.368+1249C>G		intron_variant	Intron 1 of 1	3
ENSG00000183308	ENST00000831782.1	n.586+1249C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34603 AN: 151956 Hom.: 4710 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.170

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.00886

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.181

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.228 AC: 34646 AN: 152074 Hom.: 4717 Cov.: 32 AF XY: 0.223 AC XY: 16597 AN XY: 74336

African (AFR) AF: 0.375 AC: 15548 AN: 41424

American (AMR) AF: 0.170 AC: 2593 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 824 AN: 3472

East Asian (EAS) AF: 0.00888 AC: 46 AN: 5182

South Asian (SAS) AF: 0.0831 AC: 401 AN: 4824

European-Finnish (FIN) AF: 0.181 AC: 1917 AN: 10582

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12660 AN: 67986

Other (OTH) AF: 0.220 AC: 464 AN: 2112

Alfa AF: 0.218 Hom.: 525

Bravo AF: 0.236

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.9
DANN	Benign	0.42
PhyloP100		-0.14
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs874358; hg19: chr2-201829602;