chr2-170684313-A-C

Variant names:

• chr2-170684313-A-C
• rs2080401
• ENST00000428156.1:n.389-1254T>G

Variant summary

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

The ENST00000428156.1(ENSG00000213981):​n.389-1254T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 152,020 control chromosomes in the GnomAD database, including 10,752 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 0.37 (10752 hom., cov: 32)
• Consequence: ENSG00000213981 ENST00000428156.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200
• Publications: 18 publications found

Genes affected

ENSG00000213981 (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 (AMR) allele frequency at 95% confidence interval = 0.498 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100130256	NR_187617.1	n.145-1254T>G		intron_variant	Intron 1 of 14
LOC100130256	NR_187618.1	n.145-1254T>G		intron_variant	Intron 1 of 13
LOC100130256	NR_187619.1	n.145-1254T>G		intron_variant	Intron 1 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000213981	ENST00000428156.1	n.389-1254T>G		intron_variant	Intron 1 of 9	2

Frequencies

GnomAD3 genomes AF: 0.371 AC: 56361 AN: 151902 Hom.: 10729 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.369

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

GnomAD4 genome AF: 0.371 AC: 56427 AN: 152020 Hom.: 10752 Cov.: 32 AF XY: 0.373 AC XY: 27702 AN XY: 74308

African (AFR) AF: 0.358 AC: 14864 AN: 41488

American (AMR) AF: 0.508 AC: 7749 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1010 AN: 3468

East Asian (EAS) AF: 0.285 AC: 1472 AN: 5166

South Asian (SAS) AF: 0.390 AC: 1879 AN: 4822

European-Finnish (FIN) AF: 0.386 AC: 4078 AN: 10554

Middle Eastern (MID) AF: 0.306 AC: 90 AN: 294

European-Non Finnish (NFE) AF: 0.356 AC: 24226 AN: 67956

Other (OTH) AF: 0.370 AC: 779 AN: 2108

Alfa AF: 0.359 Hom.: 33964

Bravo AF: 0.383

Asia WGS AF: 0.357 AC: 1239 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	4.6
DANN	Benign	0.73
PhyloP100		0.0020

Splicing

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

Other links and lift over

dbSNP: rs2080401; hg19: chr2-171540823;