rs2082382

Variant names:

• chr5-148820990-G-A
• rs2082382

Your query was ambiguous. Multiple possible variants found:

• chr5-148820990-G-A
• chr5-148820990-G-C
• chr5-148820990-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 0.717 in 152,164 control chromosomes in the GnomAD database, including 41,268 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 0.72 (41268 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 18 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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: 0.717 AC: 109024 AN: 152044 Hom.: 41194 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.766

Gnomad ASJ AF: 0.621

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.828

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.567

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.717 AC: 109161 AN: 152164 Hom.: 41268 Cov.: 32 AF XY: 0.726 AC XY: 53979 AN XY: 74384

African (AFR) AF: 0.925 AC: 38426 AN: 41558

American (AMR) AF: 0.767 AC: 11720 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.621 AC: 2152 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5163 AN: 5178

South Asian (SAS) AF: 0.829 AC: 3998 AN: 4824

European-Finnish (FIN) AF: 0.657 AC: 6949 AN: 10572

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.567 AC: 38508 AN: 67960

Other (OTH) AF: 0.719 AC: 1519 AN: 2114

Alfa AF: 0.633 Hom.: 21481

Bravo AF: 0.732

Asia WGS AF: 0.917 AC: 3186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	16
DANN	Benign	0.62
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs2082382; hg19: chr5-148200553;