rs880253

Variant names:

• chr2-190764960-C-T
• rs880253
• ENST00000676095.2:n.195-25629G>A

Variant summary

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

The ENST00000676095.2(ENSG00000228509):​n.195-25629G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,108 control chromosomes in the GnomAD database, including 1,430 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 0.11 (1430 hom., cov: 33)
• Consequence: ENSG00000228509 ENST00000676095.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.499
• Publications: 1 publications found

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 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
ENSG00000228509	ENST00000676095.2	n.195-25629G>A		intron_variant	Intron 2 of 8
ENSG00000228509	ENST00000772360.1	n.286-25629G>A		intron_variant	Intron 2 of 3
ENSG00000228509	ENST00000772361.1	n.181-25629G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16036 AN: 151990 Hom.: 1421 Cov.: 33

Gnomad AFR AF: 0.0853

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.0876

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.197

Gnomad FIN AF: 0.0435

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0651

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.106 AC: 16068 AN: 152108 Hom.: 1430 Cov.: 33 AF XY: 0.111 AC XY: 8250 AN XY: 74368

African (AFR) AF: 0.0853 AC: 3537 AN: 41482

American (AMR) AF: 0.287 AC: 4372 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0876 AC: 304 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1705 AN: 5162

South Asian (SAS) AF: 0.198 AC: 953 AN: 4812

European-Finnish (FIN) AF: 0.0435 AC: 461 AN: 10592

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.0651 AC: 4429 AN: 68012

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.0851 Hom.: 445

Bravo AF: 0.125

Asia WGS AF: 0.234 AC: 815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.48
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs880253; hg19: chr2-191629686;