rs3826042

Variant names:

• chr15-74726564-C-T
• rs3826042

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 0.0383 in 152,178 control chromosomes in the GnomAD database, including 167 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 0.038 (167 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0939 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: 0.0383 AC: 5826 AN: 152060 Hom.: 168 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.00330

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.115

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0490

Gnomad OTH AF: 0.0501

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

GnomAD4 genome AF: 0.0383 AC: 5825 AN: 152178 Hom.: 167 Cov.: 32 AF XY: 0.0375 AC XY: 2787 AN XY: 74390

Gnomad4 AFR AF: 0.0115

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.115

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.0251

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0490

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0390 Hom.: 19

Bravo AF: 0.0409

Asia WGS AF: 0.0550 AC: 189 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	4.9
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3826042; hg19: chr15-75018905;