rs1605683

Variant names:

• chr5-35579029-T-G
• rs1605683

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 0.277 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.249 AC: 10351 AN: 41498

American (AMR) AF: 0.235 AC: 3589 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1219 AN: 3466

East Asian (EAS) AF: 0.175 AC: 907 AN: 5172

South Asian (SAS) AF: 0.261 AC: 1260 AN: 4824

European-Finnish (FIN) AF: 0.340 AC: 3588 AN: 10564

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.298 AC: 20267 AN: 67936

Other (OTH) AF: 0.264 AC: 557 AN: 2112

Alfa AF: 0.292 Hom.: 16806

Bravo AF: 0.265

Asia WGS AF: 0.231 AC: 803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.62
PhyloP100		-0.96

Splicing

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

Other links and lift over

dbSNP: rs1605683; hg19: chr5-35579131;