2-170684313-A-C

Position:

• chr2-170684313-A-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000213981 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC100130256	NR_187617.1	n.145-1254T>G		intron_variant
LOC100130256	NR_187618.1	n.145-1254T>G		intron_variant
LOC100130256	NR_187619.1	n.145-1254T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000213981	ENST00000428156.1	n.389-1254T>G		intron_variant		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

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.508

Gnomad4 ASJ AF: 0.291

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.370

Alfa AF: 0.352 Hom.: 19739

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2080401; hg19: chr2-171540823;