rs720485

Variant names:

• chr4-144541436-A-C
• rs720485
• ENST00000649263.1:n.328-125458T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-144541436-A-C
• chr4-144541436-A-T

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-125458T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.319 in 152,110 control chromosomes in the GnomAD database, including 9,451 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 0.32 (9451 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00400
• Publications: 16 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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.473 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.328-125458T>G		intron	N/A	ENSP00000497507.1
	ENSG00000285783	ENST00000650526.1		n.223-125458T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48437 AN: 151990 Hom.: 9442 Cov.: 32

Gnomad AFR AF: 0.0953

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.319 AC: 48452 AN: 152110 Hom.: 9451 Cov.: 32 AF XY: 0.325 AC XY: 24194 AN XY: 74342

African (AFR) AF: 0.0952 AC: 3953 AN: 41538

American (AMR) AF: 0.310 AC: 4740 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3470

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5174

South Asian (SAS) AF: 0.490 AC: 2361 AN: 4820

European-Finnish (FIN) AF: 0.535 AC: 5643 AN: 10552

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27954 AN: 67964

Other (OTH) AF: 0.303 AC: 641 AN: 2114

Alfa AF: 0.379 Hom.: 5951

Bravo AF: 0.285

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.0040

Splicing

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

Other links and lift over

dbSNP: rs720485; hg19: chr4-145462588;