rs4522817

Variant names:

• chr4-4994149-G-A
• rs4522817
• ENST00000774609.1:n.268-10396G>A

Your query was ambiguous. Multiple possible variants found:

• chr4-4994149-G-A
• chr4-4994149-G-C

Variant summary

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

The ENST00000774609.1(ENSG00000300857):​n.268-10396G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.492 in 149,576 control chromosomes in the GnomAD database, including 18,648 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 0.49 (18648 hom., cov: 26)
• Consequence: ENSG00000300857 ENST00000774609.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.09
• Publications: 4 publications found

Genes affected

ENSG00000300857 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 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
ENSG00000300857	ENST00000774609.1	n.268-10396G>A		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.492 AC: 73507 AN: 149462 Hom.: 18647 Cov.: 26

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.492 AC: 73522 AN: 149576 Hom.: 18648 Cov.: 26 AF XY: 0.487 AC XY: 35469 AN XY: 72804

African (AFR) AF: 0.370 AC: 15017 AN: 40598

American (AMR) AF: 0.472 AC: 7124 AN: 15108

Ashkenazi Jewish (ASJ) AF: 0.448 AC: 1548 AN: 3452

East Asian (EAS) AF: 0.455 AC: 2293 AN: 5040

South Asian (SAS) AF: 0.433 AC: 2028 AN: 4680

European-Finnish (FIN) AF: 0.528 AC: 5241 AN: 9924

Middle Eastern (MID) AF: 0.486 AC: 140 AN: 288

European-Non Finnish (NFE) AF: 0.572 AC: 38608 AN: 67516

Other (OTH) AF: 0.475 AC: 981 AN: 2066

Alfa AF: 0.535 Hom.: 62299

Bravo AF: 0.482

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.9
DANN	Benign	0.81
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs4522817; hg19: chr4-4995876;