rs1605683

Variant names:

• chr5-35579029-T-G
• rs1605683

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 0.277 in 152,064 control chromosomes in the GnomAD database, including 5,920 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 0.28 (5920 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 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: 0.277 AC: 42055 AN: 151946 Hom.: 5925 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.249

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.340

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.277 AC: 42060 AN: 152064 Hom.: 5920 Cov.: 32 AF XY: 0.279 AC XY: 20747 AN XY: 74322

Gnomad4 AFR AF: 0.249

Gnomad4 AMR AF: 0.235

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.340

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.264

Alfa AF: 0.297 Hom.: 11057

Bravo AF: 0.265

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1605683; hg19: chr5-35579131;