rs1432982

Variant names:

• chr5-147854895-G-A
• rs1432982

Your query was ambiguous. Multiple possible variants found:

• chr5-147854895-G-A
• chr5-147854895-G-C

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 0.49 in 152,026 control chromosomes in the GnomAD database, including 21,210 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 (21210 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.490 AC: 74424 AN: 151908 Hom.: 21164 Cov.: 33

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.490 AC: 74532 AN: 152026 Hom.: 21210 Cov.: 33 AF XY: 0.486 AC XY: 36088 AN XY: 74300

African (AFR) AF: 0.783 AC: 32491 AN: 41486

American (AMR) AF: 0.396 AC: 6045 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1702 AN: 3470

East Asian (EAS) AF: 0.686 AC: 3540 AN: 5160

South Asian (SAS) AF: 0.469 AC: 2261 AN: 4820

European-Finnish (FIN) AF: 0.306 AC: 3227 AN: 10552

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23809 AN: 67968

Other (OTH) AF: 0.479 AC: 1011 AN: 2112

Alfa AF: 0.397 Hom.: 2528

Bravo AF: 0.514

Asia WGS AF: 0.615 AC: 2136 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	3.0
DANN	Benign	0.56
PhyloP100		-0.049

Splicing

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

Other links and lift over

dbSNP: rs1432982; hg19: chr5-147234458; COSMIC: COSV72842715;