rs35898099

Variant names:

• chr6-136793620-G-A
• rs35898099

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 0.186 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
• Publications: 3 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0469 AC: 1945 AN: 41484

American (AMR) AF: 0.244 AC: 3716 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.299 AC: 1038 AN: 3468

East Asian (EAS) AF: 0.0638 AC: 331 AN: 5190

South Asian (SAS) AF: 0.117 AC: 562 AN: 4818

European-Finnish (FIN) AF: 0.237 AC: 2498 AN: 10532

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.258 AC: 17565 AN: 67964

Other (OTH) AF: 0.195 AC: 411 AN: 2104

Alfa AF: 0.196 Hom.: 2681

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
PhyloP100		0.18

Splicing

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

Other links and lift over

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