rs4295402

Variant names:

• chr5-30242487-G-A
• rs4295402

Your query was ambiguous. Multiple possible variants found:

• chr5-30242487-G-A
• chr5-30242487-G-C
• chr5-30242487-G-T

Variant summary

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

The variant allele was found at a frequency of 0.539 in 151,998 control chromosomes in the GnomAD database, including 22,482 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 0.54 (22482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0520
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.819 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

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81870 AN: 151880 Hom.: 22468 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.567

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.840

Gnomad SAS AF: 0.637

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.539 AC: 81936 AN: 151998 Hom.: 22482 Cov.: 32 AF XY: 0.546 AC XY: 40571 AN XY: 74300

African (AFR) AF: 0.499 AC: 20685 AN: 41444

American (AMR) AF: 0.567 AC: 8665 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1591 AN: 3470

East Asian (EAS) AF: 0.839 AC: 4335 AN: 5164

South Asian (SAS) AF: 0.635 AC: 3065 AN: 4824

European-Finnish (FIN) AF: 0.605 AC: 6373 AN: 10542

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35641 AN: 67958

Other (OTH) AF: 0.508 AC: 1075 AN: 2116

Alfa AF: 0.532 Hom.: 90338

Bravo AF: 0.534

Asia WGS AF: 0.741 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.9
DANN	Benign	0.15
PhyloP100		0.052

Splicing

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

Other links and lift over

dbSNP: rs4295402; hg19: chr5-30242594;