rs860413

chr5-35942940-A-Cchr5-35942940-A-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 0.226 in 151,954 control chromosomes in the GnomAD database, including 4,221 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 0.23 (4221 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.272 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: 0.226 AC: 34272 AN: 151836 Hom.: 4227 Cov.: 31

Gnomad AFR AF: 0.121

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.215

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

GnomAD4 genome AF: 0.226 AC: 34269 AN: 151954 Hom.: 4221 Cov.: 31 AF XY: 0.228 AC XY: 16903 AN XY: 74250

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.212

Gnomad4 ASJ AF: 0.276

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.216

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.275

Gnomad4 OTH AF: 0.217

Alfa AF: 0.264 Hom.: 11866

Bravo AF: 0.212

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.73
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs860413; hg19: chr5-35943042;