rs860413

Variant names:

• chr5-35942940-A-C
• rs860413

Your query was ambiguous. Multiple possible variants found:

• chr5-35942940-A-C
• chr5-35942940-A-G
• chr5-35942940-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;