chr2-118044105-C-A

Variant names:

• chr2-118044105-C-A
• rs6542427
• ENST00000627626.1:n.247-10615C>A

Variant summary

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

The ENST00000747789.1(ENSG00000297418):​n.324+1496G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,888 control chromosomes in the GnomAD database, including 6,300 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 0.28 (6300 hom., cov: 32)
• Consequence: ENSG00000297418 ENST00000747789.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 6 publications found

Genes affected

ENSG00000235066 (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 (AFR) allele frequency at 95% confidence interval = 0.37 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
	ENSG00000235066	ENST00000627626.1	TSL:5	n.247-10615C>A		intron	N/A
	ENSG00000235066	ENST00000627670.3	TSL:5	n.1227-10590C>A		intron	N/A
	ENSG00000297418	ENST00000747789.1		n.324+1496G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42333 AN: 151770 Hom.: 6289 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.276

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.261

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.279 AC: 42367 AN: 151888 Hom.: 6300 Cov.: 32 AF XY: 0.276 AC XY: 20492 AN XY: 74242

African (AFR) AF: 0.375 AC: 15494 AN: 41350

American (AMR) AF: 0.214 AC: 3269 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 996 AN: 3464

East Asian (EAS) AF: 0.140 AC: 726 AN: 5178

South Asian (SAS) AF: 0.276 AC: 1327 AN: 4808

European-Finnish (FIN) AF: 0.177 AC: 1866 AN: 10572

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.261 AC: 17723 AN: 67924

Other (OTH) AF: 0.267 AC: 563 AN: 2108

Alfa AF: 0.273 Hom.: 3113

Bravo AF: 0.284

Asia WGS AF: 0.223 AC: 779 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	0.91
DANN	Benign	0.33
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs6542427; hg19: chr2-118801681;