5-35879985-G-C

Variant names:

• chr5-35879985-G-C
• rs1494571

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 0.259 in 152,074 control chromosomes in the GnomAD database, including 5,315 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 0.26 (5315 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0380
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.273 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39321 AN: 151956 Hom.: 5314 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.0741

Gnomad SAS AF: 0.199

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.259 AC: 39319 AN: 152074 Hom.: 5315 Cov.: 32 AF XY: 0.257 AC XY: 19084 AN XY: 74334

African (AFR) AF: 0.277 AC: 11484 AN: 41472

American (AMR) AF: 0.216 AC: 3307 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 920 AN: 3472

East Asian (EAS) AF: 0.0745 AC: 386 AN: 5184

South Asian (SAS) AF: 0.199 AC: 954 AN: 4806

European-Finnish (FIN) AF: 0.289 AC: 3058 AN: 10572

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18258 AN: 67972

Other (OTH) AF: 0.261 AC: 549 AN: 2102

Alfa AF: 0.114 Hom.: 209

Bravo AF: 0.253

Asia WGS AF: 0.149 AC: 519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.6
DANN	Benign	0.70
PhyloP100		0.038

Splicing

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

Other links and lift over

dbSNP: rs1494571; hg19: chr5-35880087;