4-144575789-A-G

Position:

• chr4-144575789-A-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.144575789A>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-159811T>C		intron_variant				ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-159811T>C		intron_variant

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

Gnomad4 AFR AF: 0.988

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.912

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.982

Gnomad4 FIN AF: 0.942

Gnomad4 NFE AF: 0.940

Gnomad4 OTH AF: 0.947

Alfa AF: 0.945 Hom.: 31453

Bravo AF: 0.958

Asia WGS AF: 0.988 AC: 3438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2175586; hg19: chr4-145496941;