rs42868

Variant names:

• chr5-33935971-C-G
• rs42868

Your query was ambiguous. Multiple possible variants found:

• chr5-33935971-C-G
• chr5-33935971-C-T

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 0.218 in 152,216 control chromosomes in the GnomAD database, including 4,218 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 0.22 (4218 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.218
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 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: 0.218 AC: 33213 AN: 152098 Hom.: 4209 Cov.: 33

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.140

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0499

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.179

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.218 AC: 33244 AN: 152216 Hom.: 4218 Cov.: 33 AF XY: 0.214 AC XY: 15957 AN XY: 74452

African (AFR) AF: 0.356 AC: 14789 AN: 41510

American (AMR) AF: 0.139 AC: 2134 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 382 AN: 3470

East Asian (EAS) AF: 0.0500 AC: 259 AN: 5180

South Asian (SAS) AF: 0.132 AC: 637 AN: 4832

European-Finnish (FIN) AF: 0.216 AC: 2290 AN: 10604

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12165 AN: 68004

Other (OTH) AF: 0.172 AC: 363 AN: 2114

Alfa AF: 0.210 Hom.: 490

Bravo AF: 0.217

Asia WGS AF: 0.119 AC: 415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.33
DANN	Benign	0.38
PhyloP100		-0.22
PromoterAI		-0.12	Neutral

Splicing

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

Other links and lift over

dbSNP: rs42868; hg19: chr5-33936076;