ENST00000438963.2:n.247+67091G>C

Variant names:

• chr2-175324679-G-C
• rs920557
• ENST00000438963.2:n.247+67091G>C

Variant summary

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

The ENST00000438963.2(ENSG00000229066):​n.247+67091G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,198 control chromosomes in the GnomAD database, including 2,686 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 0.18 (2686 hom., cov: 32)
• Consequence: ENSG00000229066 ENST00000438963.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.143
• Publications: 3 publications found

Genes affected

ENSG00000229066 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000438963.2. 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
	ENSG00000229066	ENST00000438963.2	TSL:3	n.247+67091G>C		intron	N/A
	ENSG00000229066	ENST00000444567.1	TSL:3	n.448+33178G>C		intron	N/A
	ENSG00000229066	ENST00000653625.1		n.336+33178G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27851 AN: 152080 Hom.: 2671 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.183 AC: 27906 AN: 152198 Hom.: 2686 Cov.: 32 AF XY: 0.186 AC XY: 13838 AN XY: 74412

African (AFR) AF: 0.145 AC: 6040 AN: 41524

American (AMR) AF: 0.229 AC: 3502 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 738 AN: 3462

East Asian (EAS) AF: 0.377 AC: 1952 AN: 5180

South Asian (SAS) AF: 0.211 AC: 1019 AN: 4824

European-Finnish (FIN) AF: 0.167 AC: 1768 AN: 10592

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12165 AN: 68004

Other (OTH) AF: 0.212 AC: 449 AN: 2114

Alfa AF: 0.0770 Hom.: 94

Bravo AF: 0.188

Asia WGS AF: 0.296 AC: 1029 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.9
DANN	Benign	0.44
PhyloP100		0.14
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		0.99

Splicing

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

Other links and lift over

dbSNP: rs920557; hg19: chr2-176189407;