rs1662840

chr4-81235255-C-T

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 0.374 in 152,034 control chromosomes in the GnomAD database, including 13,820 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 0.37 (13820 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.473

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56805 AN: 151916 Hom.: 13794 Cov.: 32

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.374 AC: 56891 AN: 152034 Hom.: 13820 Cov.: 32 AF XY: 0.366 AC XY: 27198 AN XY: 74336

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.324

Alfa AF: 0.369 Hom.: 2439

Bravo AF: 0.393

Asia WGS AF: 0.218 AC: 761 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	13
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1662840; hg19: chr4-82156409;