rs3826042

chr15-74726564-C-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 0.0383 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;