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: 15 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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285713	ENST00000649263.1		n.*44-53343A>C		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000648340.1		n.215-53343A>C		intron	N/A
	ENSG00000285783	ENST00000650526.1		n.299-53343A>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2202507;

hg19: chr4-145257681;