chr4-144513536-T-C

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.165-14016A>G		intron_variant	Intron 1 of 7
LOC105377462	XR_939273.3	n.164+48448A>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-97558A>G		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-97558A>G		intron_variant	Intron 2 of 14

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 v4.3

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

Other links and lift over

dbSNP: rs1032296; hg19: chr4-145434688;