rs1032296

Variant names:

• chr4-144513536-T-C
• rs1032296
• ENST00000649263.1:n.328-97558A>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-97558A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,086 control chromosomes in the GnomAD database, including 36,473 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 0.68 (36473 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05
• Publications: 19 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=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.844 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.328-97558A>G		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.223-97558A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103708 AN: 151968 Hom.: 36425 Cov.: 33

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.546

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.676

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.632

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

GnomAD4 genome AF: 0.683 AC: 103819 AN: 152086 Hom.: 36473 Cov.: 33 AF XY: 0.687 AC XY: 51086 AN XY: 74340

African (AFR) AF: 0.837 AC: 34739 AN: 41512

American (AMR) AF: 0.661 AC: 10090 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.546 AC: 1896 AN: 3472

East Asian (EAS) AF: 0.619 AC: 3187 AN: 5146

South Asian (SAS) AF: 0.866 AC: 4172 AN: 4820

European-Finnish (FIN) AF: 0.676 AC: 7153 AN: 10580

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40545 AN: 67968

Other (OTH) AF: 0.633 AC: 1335 AN: 2110

Alfa AF: 0.622 Hom.: 36891

Bravo AF: 0.677

Asia WGS AF: 0.786 AC: 2733 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.43
PhyloP100		-2.1

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1032296;

hg19: chr4-145434688;