rs3935914

Variant names:

• chr6-115807266-G-A
• rs3935914

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 0.235 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.203 AC: 8403 AN: 41456

American (AMR) AF: 0.191 AC: 2915 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1044 AN: 5156

South Asian (SAS) AF: 0.316 AC: 1525 AN: 4826

European-Finnish (FIN) AF: 0.182 AC: 1927 AN: 10566

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.264 AC: 17904 AN: 67938

Other (OTH) AF: 0.235 AC: 495 AN: 2110

Alfa AF: 0.251 Hom.: 638

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
PhyloP100		0.47

Splicing

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

Other links and lift over

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