chr4-144513432-T-G

Variant names:

• chr4-144513432-T-G
• rs1032295
• ENST00000649263.1:n.328-97454A>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-97454A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,716 control chromosomes in the GnomAD database, including 9,267 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 0.33 (9267 hom., cov: 31)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0150
• Publications: 12 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 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.328-97454A>C		intron	N/A	ENSP00000497507.1
	ENSG00000285783	ENST00000650526.1		n.223-97454A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49396 AN: 151598 Hom.: 9264 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.249

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.326 AC: 49402 AN: 151716 Hom.: 9267 Cov.: 31 AF XY: 0.330 AC XY: 24483 AN XY: 74110

African (AFR) AF: 0.147 AC: 6076 AN: 41378

American (AMR) AF: 0.281 AC: 4277 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1275 AN: 3466

East Asian (EAS) AF: 0.249 AC: 1274 AN: 5120

South Asian (SAS) AF: 0.523 AC: 2513 AN: 4806

European-Finnish (FIN) AF: 0.503 AC: 5284 AN: 10512

Middle Eastern (MID) AF: 0.466 AC: 135 AN: 290

European-Non Finnish (NFE) AF: 0.405 AC: 27502 AN: 67882

Other (OTH) AF: 0.325 AC: 686 AN: 2108

Alfa AF: 0.378 Hom.: 23006

Bravo AF: 0.291

Asia WGS AF: 0.347 AC: 1206 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.45
DANN	Benign	0.61
PhyloP100		-0.015

Splicing

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

Other links and lift over

dbSNP: rs1032295; hg19: chr4-145434584;