rs4495224

Variant names:

• chr5-40477413-C-A
• rs4495224
• ENST00000648975.1:n.2650+450G>T

Your query was ambiguous. Multiple possible variants found:

• chr5-40477413-C-A
• chr5-40477413-C-G

Variant summary

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

The ENST00000648975.1(ENSG00000285616):​n.2650+450G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.606 in 151,828 control chromosomes in the GnomAD database, including 28,502 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 0.61 (28502 hom., cov: 31)
• Consequence: ENSG00000285616 ENST00000648975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0420
• Publications: 19 publications found

Genes affected

ENSG00000285616 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.63).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.66 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285616	ENST00000648975.1	n.2650+450G>T		intron_variant	Intron 2 of 2
ENSG00000285552	ENST00000649444.1	n.120-8963C>A		intron_variant	Intron 1 of 2
ENSG00000285552	ENST00000649894.1	n.119+13733C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.606 AC: 91977 AN: 151710 Hom.: 28474 Cov.: 31

Gnomad AFR AF: 0.579

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.574

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.606 AC: 92056 AN: 151828 Hom.: 28502 Cov.: 31 AF XY: 0.599 AC XY: 44406 AN XY: 74162

African (AFR) AF: 0.579 AC: 23945 AN: 41390

American (AMR) AF: 0.585 AC: 8925 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2211 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1223 AN: 5154

South Asian (SAS) AF: 0.478 AC: 2297 AN: 4810

European-Finnish (FIN) AF: 0.574 AC: 6037 AN: 10524

Middle Eastern (MID) AF: 0.687 AC: 202 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45196 AN: 67920

Other (OTH) AF: 0.622 AC: 1310 AN: 2106

Alfa AF: 0.644 Hom.: 5103

Bravo AF: 0.607

Asia WGS AF: 0.400 AC: 1390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	4.2
DANN	Benign	0.66
PhyloP100		-0.042

Splicing

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

Other links and lift over

dbSNP: rs4495224; hg19: chr5-40477515;