chr2-155400189-G-A

Variant names:

• chr2-155400189-G-A
• rs4544377
• ENST00000808398.1:n.67-4077G>A

Variant summary

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

The ENST00000808398.1(ENSG00000305077):​n.67-4077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,112 control chromosomes in the GnomAD database, including 52,662 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 0.83 (52662 hom., cov: 32)
• Consequence: ENSG00000305077 ENST00000808398.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 5 publications found

Genes affected

ENSG00000305077 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.881 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373699	XR_923496.2	n.223-4077G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305077	ENST00000808398.1	n.67-4077G>A		intron_variant	Intron 1 of 4
ENSG00000305077	ENST00000808399.1	n.53-4077G>A		intron_variant	Intron 1 of 3
ENSG00000305077	ENST00000808400.1	n.79-4077G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.829 AC: 125994 AN: 151994 Hom.: 52627 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.821

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.867

Gnomad NFE AF: 0.887

Gnomad OTH AF: 0.833

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

GnomAD4 genome AF: 0.829 AC: 126079 AN: 152112 Hom.: 52662 Cov.: 32 AF XY: 0.828 AC XY: 61541 AN XY: 74368

African (AFR) AF: 0.712 AC: 29554 AN: 41490

American (AMR) AF: 0.867 AC: 13243 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3041 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4366 AN: 5160

South Asian (SAS) AF: 0.821 AC: 3967 AN: 4830

European-Finnish (FIN) AF: 0.832 AC: 8812 AN: 10596

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.887 AC: 60316 AN: 67976

Other (OTH) AF: 0.830 AC: 1752 AN: 2112

Alfa AF: 0.862 Hom.: 37962

Bravo AF: 0.825

Asia WGS AF: 0.829 AC: 2879 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.17
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs4544377; hg19: chr2-156256701;