chr2-112822855-C-G

Variant names:

• chr2-112822855-C-G
• rs3917375
• ENST00000670671.2:n.222+1406G>C

Variant summary

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

The ENST00000670671.2(ENSG00000287937):​n.222+1406G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 152,198 control chromosomes in the GnomAD database, including 52,332 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 0.82 (52332 hom., cov: 32)
• Consequence: ENSG00000287937 ENST00000670671.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31
• Publications: 0 publications found

Genes affected

ENSG00000287937 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.914 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000670671.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287937	ENST00000670671.2		n.222+1406G>C		intron	N/A
	ENSG00000299339	ENST00000762706.1		n.404+51959C>G		intron	N/A
	ENSG00000299339	ENST00000762707.1		n.499+51959C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.817 AC: 124241 AN: 152080 Hom.: 52294 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.962

Gnomad AMR AF: 0.833

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.940

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.920

Gnomad OTH AF: 0.834

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

GnomAD4 genome AF: 0.817 AC: 124323 AN: 152198 Hom.: 52332 Cov.: 32 AF XY: 0.818 AC XY: 60898 AN XY: 74424

African (AFR) AF: 0.594 AC: 24641 AN: 41468

American (AMR) AF: 0.833 AC: 12736 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3103 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4752 AN: 5188

South Asian (SAS) AF: 0.760 AC: 3668 AN: 4824

European-Finnish (FIN) AF: 0.940 AC: 9972 AN: 10614

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.920 AC: 62574 AN: 68026

Other (OTH) AF: 0.835 AC: 1759 AN: 2106

Alfa AF: 0.869 Hom.: 6865

Bravo AF: 0.802

Asia WGS AF: 0.826 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.45
PhyloP100		-1.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3917375;

hg19: chr2-113580432;