rs3935914

chr6-115807266-G-A

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 0.235 in 151,968 control chromosomes in the GnomAD database, including 4,395 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 0.24 (4395 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.471

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.303 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: 0.235 AC: 35740 AN: 151850 Hom.: 4389 Cov.: 31

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.417

Gnomad AMR AF: 0.191

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.264

Gnomad OTH AF: 0.233

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

GnomAD4 genome AF: 0.235 AC: 35763 AN: 151968 Hom.: 4395 Cov.: 31 AF XY: 0.232 AC XY: 17223 AN XY: 74304

Gnomad4 AFR AF: 0.203

Gnomad4 AMR AF: 0.191

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.182

Gnomad4 NFE AF: 0.264

Gnomad4 OTH AF: 0.235

Alfa AF: 0.253 Hom.: 625

Bravo AF: 0.231

Asia WGS AF: 0.248 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.8
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3935914; hg19: chr6-116128430; COSMIC: COSV69421681;