rs2235715

Variant names:

• chr6-1598707-C-T
• rs2235715

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 0.148 in 152,258 control chromosomes in the GnomAD database, including 2,221 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 0.15 (2221 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.287 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: 0.148 AC: 22551 AN: 152140 Hom.: 2209 Cov.: 33

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.240

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.148 AC: 22582 AN: 152258 Hom.: 2221 Cov.: 33 AF XY: 0.153 AC XY: 11421 AN XY: 74448

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.294

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.181

Alfa AF: 0.172 Hom.: 2787

Bravo AF: 0.157

Asia WGS AF: 0.191 AC: 665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2235715; hg19: chr6-1598942;