rs4702522

Variant names:

• chr5-4194086-A-G
• rs4702522
• ENST00000762810.1:n.332-51A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-4194086-A-G
• chr5-4194086-A-T

Variant summary

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

The ENST00000762810.1(ENSG00000299354):​n.332-51A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.947 in 152,284 control chromosomes in the GnomAD database, including 68,392 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 0.95 (68392 hom., cov: 33)
• Consequence: ENSG00000299354 ENST00000762810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.920
• Publications: 1 publications found

Genes affected

ENSG00000299354 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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
ENSG00000299354	ENST00000762810.1	n.332-51A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.947 AC: 144157 AN: 152166 Hom.: 68345 Cov.: 33

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.962

Gnomad ASJ AF: 0.956

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.982

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.950

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.947 AC: 144256 AN: 152284 Hom.: 68392 Cov.: 33 AF XY: 0.949 AC XY: 70650 AN XY: 74480

African (AFR) AF: 0.927 AC: 38516 AN: 41540

American (AMR) AF: 0.962 AC: 14722 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.956 AC: 3316 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5155 AN: 5186

South Asian (SAS) AF: 0.904 AC: 4361 AN: 4824

European-Finnish (FIN) AF: 0.982 AC: 10423 AN: 10616

Middle Eastern (MID) AF: 0.952 AC: 278 AN: 292

European-Non Finnish (NFE) AF: 0.950 AC: 64636 AN: 68034

Other (OTH) AF: 0.936 AC: 1976 AN: 2112

Alfa AF: 0.950 Hom.: 9596

Bravo AF: 0.946

Asia WGS AF: 0.919 AC: 3198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.16
DANN	Benign	0.21
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs4702522; hg19: chr5-4194199;