rs2202507

Variant names:

• chr4-144336529-T-G
• rs2202507
• ENST00000649263.1:n.*44-53343A>C

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.*44-53343A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 151,970 control chromosomes in the GnomAD database, including 14,361 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 0.40 (14361 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 14 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 (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.315-53343A>C		intron_variant	Intron 3 of 7
LOC105377462	XR_939273.3	n.241-53343A>C		intron_variant	Intron 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.*44-53343A>C		intron_variant	Intron 5 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000648340.1	n.215-53343A>C		intron_variant	Intron 2 of 5
ENSG00000285783	ENST00000650526.1	n.299-53343A>C		intron_variant	Intron 3 of 14
GUSBP5	ENST00000651102.1	n.1992-5630T>G		intron_variant	Intron 13 of 14

Frequencies

GnomAD3 genomes AF: 0.404 AC: 61420 AN: 151852 Hom.: 14344 Cov.: 32

Gnomad AFR AF: 0.162

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.429

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.404 AC: 61446 AN: 151970 Hom.: 14361 Cov.: 32 AF XY: 0.410 AC XY: 30470 AN XY: 74256

African (AFR) AF: 0.162 AC: 6725 AN: 41490

American (AMR) AF: 0.470 AC: 7168 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1434 AN: 3466

East Asian (EAS) AF: 0.429 AC: 2208 AN: 5150

South Asian (SAS) AF: 0.597 AC: 2875 AN: 4816

European-Finnish (FIN) AF: 0.564 AC: 5942 AN: 10530

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.496 AC: 33732 AN: 67948

Other (OTH) AF: 0.388 AC: 818 AN: 2110

Alfa AF: 0.476 Hom.: 14205

Bravo AF: 0.382

Asia WGS AF: 0.505 AC: 1758 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	0.54
DANN	Benign	0.45
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs2202507; hg19: chr4-145257681;