rs584438

Variant names:

• chr17-40442920-C-A
• rs584438

Your query was ambiguous. Multiple possible variants found:

• chr17-40442920-C-A
• chr17-40442920-C-G
• chr17-40442920-C-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 0.321 in 152,176 control chromosomes in the GnomAD database, including 9,530 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 0.32 (9530 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.56).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.499 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: 0.322 AC: 48903 AN: 152058 Hom.: 9525 Cov.: 32

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.346

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.321 AC: 48914 AN: 152176 Hom.: 9530 Cov.: 32 AF XY: 0.331 AC XY: 24649 AN XY: 74406

African (AFR) AF: 0.108 AC: 4498 AN: 41552

American (AMR) AF: 0.469 AC: 7174 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.346 AC: 1200 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2535 AN: 5154

South Asian (SAS) AF: 0.516 AC: 2490 AN: 4824

European-Finnish (FIN) AF: 0.420 AC: 4456 AN: 10606

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25479 AN: 67960

Other (OTH) AF: 0.349 AC: 738 AN: 2114

Alfa AF: 0.349 Hom.: 16125

Bravo AF: 0.316

Asia WGS AF: 0.456 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.56
CADD	Benign	9.3
DANN	Benign	0.85
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs584438; hg19: chr17-38599172;