2-122383969-A-G

Variant names:

• chr2-122383969-A-G
• rs4848768
• ENST00000657880.2:n.756-148882A>G

Variant summary

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

The ENST00000657880.2(ENSG00000286481):​n.756-148882A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,116 control chromosomes in the GnomAD database, including 3,471 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 0.19 (3471 hom., cov: 32)
• Consequence: ENSG00000286481 ENST00000657880.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.964
• Publications: 5 publications found

Genes affected

ENSG00000286481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657880.2. 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
	ENSG00000286481	ENST00000657880.2		n.756-148882A>G		intron	N/A
	ENSG00000286481	ENST00000819524.1		n.102-8994A>G		intron	N/A
	ENSG00000286481	ENST00000819525.1		n.169-8994A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.189 AC: 28769 AN: 151998 Hom.: 3448 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.190 AC: 28847 AN: 152116 Hom.: 3471 Cov.: 32 AF XY: 0.193 AC XY: 14324 AN XY: 74364

African (AFR) AF: 0.275 AC: 11390 AN: 41468

American (AMR) AF: 0.257 AC: 3927 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 614 AN: 3470

East Asian (EAS) AF: 0.463 AC: 2386 AN: 5156

South Asian (SAS) AF: 0.228 AC: 1097 AN: 4812

European-Finnish (FIN) AF: 0.127 AC: 1344 AN: 10588

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7509 AN: 68022

Other (OTH) AF: 0.190 AC: 400 AN: 2108

Alfa AF: 0.165 Hom.: 4503

Bravo AF: 0.207

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.42
PhyloP100		0.96

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: rs4848768;

hg19: chr2-123141545;