5-35942940-A-C

Variant names:

• chr5-35942940-A-C
• rs860413

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 0.226 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
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.120 AC: 4988 AN: 41452

American (AMR) AF: 0.212 AC: 3228 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 958 AN: 3466

East Asian (EAS) AF: 0.163 AC: 843 AN: 5166

South Asian (SAS) AF: 0.216 AC: 1039 AN: 4804

European-Finnish (FIN) AF: 0.346 AC: 3644 AN: 10536

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18700 AN: 67966

Other (OTH) AF: 0.217 AC: 457 AN: 2108

Alfa AF: 0.257 Hom.: 23714

Bravo AF: 0.212

Asia WGS AF: 0.225 AC: 784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.73
DANN	Benign	0.72
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs860413; hg19: chr5-35943042;