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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.164+20548T>G		intron_variant	Intron 1 of 7
LOC105377462	XR_939273.3	n.164+20548T>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-125458T>G		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-125458T>G		intron_variant	Intron 2 of 14

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 v4.3

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;