rs35898099

Positions:

• chr6-136793620-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 0.186 in 152,024 control chromosomes in the GnomAD database, including 3,310 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 0.19 (3310 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.186 AC: 28310 AN: 151906 Hom.: 3310 Cov.: 31

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.299

Gnomad EAS AF: 0.0634

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.197

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

GnomAD4 genome AF: 0.186 AC: 28310 AN: 152024 Hom.: 3310 Cov.: 31 AF XY: 0.186 AC XY: 13790 AN XY: 74310

Gnomad4 AFR AF: 0.0469

Gnomad4 AMR AF: 0.244

Gnomad4 ASJ AF: 0.299

Gnomad4 EAS AF: 0.0638

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.195

Alfa AF: 0.231 Hom.: 924

Bravo AF: 0.181

Asia WGS AF: 0.0830 AC: 291 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	6.5
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35898099; hg19: chr6-137114758; COSMIC: COSV62888063;