2-112819325-A-G

Position:

• chr2-112819325-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000670671.1(ENSG00000287937):​n.313T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,652 control chromosomes in the GnomAD database, including 27,884 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 0.57 (27884 hom., cov: 28)
• Consequence: ENST00000670671.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124907871	XR_007087195.1	n.335T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000670671.1	n.313T>C		non_coding_transcript_exon_variant	2/2

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87068 AN: 151534 Hom.: 27872 Cov.: 28

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.916

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.593

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

GnomAD4 genome AF: 0.574 AC: 87102 AN: 151652 Hom.: 27884 Cov.: 28 AF XY: 0.577 AC XY: 42736 AN XY: 74054

Gnomad4 AFR AF: 0.270

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.916

Gnomad4 SAS AF: 0.586

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.593

Alfa AF: 0.668 Hom.: 46241

Bravo AF: 0.564

Asia WGS AF: 0.698 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.92
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4849124; hg19: chr2-113576902;