4-144575789-A-G

Variant names:

• chr4-144575789-A-G
• rs2175586
• ENST00000649263.1:n.328-159811T>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-159811T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.957 in 152,234 control chromosomes in the GnomAD database, including 69,765 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 0.96 (69765 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.868
• Publications: 4 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.98 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.328-159811T>C		intron	N/A	ENSP00000497507.1
	ENSG00000285783	ENST00000650526.1		n.223-159811T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.957 AC: 145583 AN: 152116 Hom.: 69703 Cov.: 31

Gnomad AFR AF: 0.989

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.982

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.947

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

GnomAD4 genome AF: 0.957 AC: 145704 AN: 152234 Hom.: 69765 Cov.: 31 AF XY: 0.958 AC XY: 71276 AN XY: 74406

African (AFR) AF: 0.988 AC: 41064 AN: 41544

American (AMR) AF: 0.949 AC: 14500 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3166 AN: 3470

East Asian (EAS) AF: 1.00 AC: 5176 AN: 5178

South Asian (SAS) AF: 0.982 AC: 4733 AN: 4820

European-Finnish (FIN) AF: 0.942 AC: 9985 AN: 10596

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63916 AN: 68030

Other (OTH) AF: 0.947 AC: 1999 AN: 2110

Alfa AF: 0.950 Hom.: 41902

Bravo AF: 0.958

Asia WGS AF: 0.988 AC: 3438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	10
DANN	Benign	0.44
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs2175586; hg19: chr4-145496941;