rs1001684

chr5-40810324-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.297 in 151,986 control chromosomes in the GnomAD database, including 7,023 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 0.30 (7023 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.193

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.297 AC: 45113 AN: 151868 Hom.: 7017 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.532

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.297 AC: 45138 AN: 151986 Hom.: 7023 Cov.: 32 AF XY: 0.300 AC XY: 22310 AN XY: 74290

Gnomad4 AFR AF: 0.351

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.532

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.259

Gnomad4 NFE AF: 0.252

Gnomad4 OTH AF: 0.295

Alfa AF: 0.264 Hom.: 7088

Bravo AF: 0.299

Asia WGS AF: 0.383 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	1.1
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1001684; hg19: chr5-40810426;