chr2-118081441-G-A

Variant names:

• chr2-118081441-G-A
• rs17047728
• ENST00000747789.1:n.231+6072C>T

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.231+6072C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,188 control chromosomes in the GnomAD database, including 1,367 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 0.12 (1367 hom., cov: 33)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 0 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.279 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

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
	ENSG00000297418	ENST00000747789.1		n.231+6072C>T		intron	N/A
	ENSG00000297418	ENST00000747790.1		n.104+6810C>T		intron	N/A
	ENSG00000297418	ENST00000747791.1		n.271+6072C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 18949 AN: 152070 Hom.: 1367 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0913

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.125 AC: 18954 AN: 152188 Hom.: 1367 Cov.: 33 AF XY: 0.124 AC XY: 9251 AN XY: 74414

African (AFR) AF: 0.145 AC: 6017 AN: 41520

American (AMR) AF: 0.191 AC: 2913 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 404 AN: 3470

East Asian (EAS) AF: 0.291 AC: 1507 AN: 5174

South Asian (SAS) AF: 0.138 AC: 665 AN: 4822

European-Finnish (FIN) AF: 0.0839 AC: 889 AN: 10602

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

European-Non Finnish (NFE) AF: 0.0912 AC: 6205 AN: 68000

Other (OTH) AF: 0.116 AC: 246 AN: 2112

Alfa AF: 0.109 Hom.: 112

Bravo AF: 0.138

Asia WGS AF: 0.176 AC: 609 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	1.7
DANN	Benign	0.85
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs17047728; hg19: chr2-118839017;