rs1001684

Variant names:

• chr5-40810324-C-A
• rs1001684

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 0.297 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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.351 AC: 14548 AN: 41444

American (AMR) AF: 0.268 AC: 4089 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1265 AN: 3466

East Asian (EAS) AF: 0.532 AC: 2738 AN: 5148

South Asian (SAS) AF: 0.339 AC: 1631 AN: 4818

European-Finnish (FIN) AF: 0.259 AC: 2739 AN: 10566

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.252 AC: 17110 AN: 67962

Other (OTH) AF: 0.295 AC: 622 AN: 2108

Alfa AF: 0.265 Hom.: 9180

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs1001684; hg19: chr5-40810426;