4-144564763-T-C

Variant names:

• chr4-144564763-T-C
• rs7655625
• ENST00000649263.1:n.328-148785A>G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-148785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 151,964 control chromosomes in the GnomAD database, including 11,643 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 0.39 (11643 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201
• Publications: 21 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 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.328-148785A>G		intron	N/A	ENSP00000497507.1
	ENSG00000285783	ENST00000650526.1		n.223-148785A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58694 AN: 151844 Hom.: 11633 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.300

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.348

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

GnomAD4 genome AF: 0.386 AC: 58719 AN: 151964 Hom.: 11643 Cov.: 32 AF XY: 0.392 AC XY: 29091 AN XY: 74286

African (AFR) AF: 0.328 AC: 13605 AN: 41456

American (AMR) AF: 0.327 AC: 4994 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1255 AN: 3468

East Asian (EAS) AF: 0.300 AC: 1540 AN: 5138

South Asian (SAS) AF: 0.493 AC: 2373 AN: 4818

European-Finnish (FIN) AF: 0.537 AC: 5667 AN: 10560

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.413 AC: 28077 AN: 67942

Other (OTH) AF: 0.347 AC: 733 AN: 2110

Alfa AF: 0.390 Hom.: 28731

Bravo AF: 0.360

Asia WGS AF: 0.373 AC: 1300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.1
DANN	Benign	0.43
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7655625; hg19: chr4-145485915;