4-144275053-A-T

Variant names:

• chr4-144275053-A-T
• rs7690204
• ENST00000649263.1:n.*135+8042T>A

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.*135+8042T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.461 in 151,910 control chromosomes in the GnomAD database, including 16,464 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 0.46 (16464 hom., cov: 33)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214
• Publications: 6 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 (AFR) allele frequency at 95% confidence interval = 0.501 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.406+8042T>A		intron_variant	Intron 4 of 7
LOC105377462	XR_939273.3	n.332+8042T>A		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.*135+8042T>A		intron_variant	Intron 6 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000648340.1	n.306+8042T>A		intron_variant	Intron 3 of 5
ENSG00000285783	ENST00000650526.1	n.390+8042T>A		intron_variant	Intron 4 of 14
GUSBP5	ENST00000651102.1	n.1926-41758A>T		intron_variant	Intron 12 of 14

Frequencies

GnomAD3 genomes AF: 0.461 AC: 69970 AN: 151792 Hom.: 16437 Cov.: 33

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.362

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.471

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

GnomAD4 genome AF: 0.461 AC: 70027 AN: 151910 Hom.: 16464 Cov.: 33 AF XY: 0.453 AC XY: 33640 AN XY: 74222

African (AFR) AF: 0.506 AC: 20995 AN: 41458

American (AMR) AF: 0.404 AC: 6168 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1749 AN: 3470

East Asian (EAS) AF: 0.362 AC: 1862 AN: 5140

South Asian (SAS) AF: 0.264 AC: 1272 AN: 4822

European-Finnish (FIN) AF: 0.385 AC: 4067 AN: 10570

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.476 AC: 32340 AN: 67876

Other (OTH) AF: 0.463 AC: 979 AN: 2114

Alfa AF: 0.463 Hom.: 2046

Bravo AF: 0.466

Asia WGS AF: 0.301 AC: 1043 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	0.58
DANN	Benign	0.42
PhyloP100		-0.21

Splicing

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

Other links and lift over

dbSNP: rs7690204; hg19: chr4-145196206;