chr2-118087695-T-C

Variant names:

• chr2-118087695-T-C
• rs4848492
• ENST00000747789.1:n.134-85A>G

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.134-85A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,050 control chromosomes in the GnomAD database, including 1,838 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 0.14 (1838 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295
• Publications: 3 publications found

Genes affected

ENSG00000297418 (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 (EAS) allele frequency at 95% confidence interval = 0.317 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000747789.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297418	ENST00000747789.1		n.134-85A>G		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+556A>G		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.174-85A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21382 AN: 151932 Hom.: 1838 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0879

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.0823

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0881

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.141 AC: 21392 AN: 152050 Hom.: 1838 Cov.: 32 AF XY: 0.140 AC XY: 10382 AN XY: 74330

African (AFR) AF: 0.204 AC: 8467 AN: 41474

American (AMR) AF: 0.193 AC: 2946 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.115 AC: 399 AN: 3468

East Asian (EAS) AF: 0.330 AC: 1704 AN: 5156

South Asian (SAS) AF: 0.135 AC: 651 AN: 4828

European-Finnish (FIN) AF: 0.0823 AC: 870 AN: 10566

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.0881 AC: 5990 AN: 67964

Other (OTH) AF: 0.122 AC: 257 AN: 2106

Alfa AF: 0.118 Hom.: 192

Bravo AF: 0.156

Asia WGS AF: 0.196 AC: 680 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.6
DANN	Benign	0.76
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4848492; hg19: chr2-118845271; COSMIC: COSV107192159;