2-118080705-A-G

Variant names:

• chr2-118080705-A-G
• rs2161830
• ENST00000747789.1:n.231+6808T>C

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+6808T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 152,066 control chromosomes in the GnomAD database, including 29,908 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 0.63 (29908 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.327
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.671 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297418	ENST00000747789.1		n.231+6808T>C		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+7546T>C		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.272-6152T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.625 AC: 95035 AN: 151948 Hom.: 29874 Cov.: 32

Gnomad AFR AF: 0.678

Gnomad AMI AF: 0.722

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.639

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.612

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.626 AC: 95124 AN: 152066 Hom.: 29908 Cov.: 32 AF XY: 0.627 AC XY: 46647 AN XY: 74344

African (AFR) AF: 0.678 AC: 28091 AN: 41462

American (AMR) AF: 0.632 AC: 9651 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 2016 AN: 3472

East Asian (EAS) AF: 0.639 AC: 3307 AN: 5174

South Asian (SAS) AF: 0.681 AC: 3285 AN: 4822

European-Finnish (FIN) AF: 0.612 AC: 6464 AN: 10560

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40236 AN: 67990

Other (OTH) AF: 0.593 AC: 1252 AN: 2112

Alfa AF: 0.598 Hom.: 86373

Bravo AF: 0.625

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.77
DANN	Benign	0.55
PhyloP100		-0.33

Splicing

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

Other links and lift over

dbSNP: rs2161830; hg19: chr2-118838281; COSMIC: COSV60100142;