rs382098

Variant names:

• chr5-63998870-A-C
• rs382098

Your query was ambiguous. Multiple possible variants found:

• chr5-63998870-A-C
• chr5-63998870-A-G
• chr5-63998870-A-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 0.588 in 152,014 control chromosomes in the GnomAD database, including 27,021 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 0.59 (27021 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.788 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: 0.588 AC: 89265 AN: 151896 Hom.: 26983 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.548

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.462

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.515

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.588 AC: 89354 AN: 152014 Hom.: 27021 Cov.: 32 AF XY: 0.586 AC XY: 43518 AN XY: 74290

African (AFR) AF: 0.711 AC: 29496 AN: 41472

American (AMR) AF: 0.595 AC: 9076 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.548 AC: 1903 AN: 3472

East Asian (EAS) AF: 0.809 AC: 4177 AN: 5166

South Asian (SAS) AF: 0.570 AC: 2743 AN: 4814

European-Finnish (FIN) AF: 0.462 AC: 4880 AN: 10572

Middle Eastern (MID) AF: 0.646 AC: 190 AN: 294

European-Non Finnish (NFE) AF: 0.515 AC: 35004 AN: 67946

Other (OTH) AF: 0.594 AC: 1247 AN: 2100

Alfa AF: 0.529 Hom.: 22310

Bravo AF: 0.605

Asia WGS AF: 0.682 AC: 2373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.49
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs382098; hg19: chr5-63294697;