2-118087695-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985940	XR_001739662.3	n.181+556A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297418	ENST00000747789.1	n.134-85A>G		intron_variant	Intron 1 of 4
ENSG00000297418	ENST00000747790.1	n.104+556A>G		intron_variant	Intron 1 of 2
ENSG00000297418	ENST00000747791.1	n.174-85A>G		intron_variant	Intron 1 of 4

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 v4.3

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;