rs1355459

chr6-23871472-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 0.314 in 151,784 control chromosomes in the GnomAD database, including 7,816 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 0.31 (7816 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

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 (SAS) allele frequency at 95% confidence interval = 0.362 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: 0.314 AC: 47688 AN: 151668 Hom.: 7807 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0788

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.314 AC: 47731 AN: 151784 Hom.: 7816 Cov.: 32 AF XY: 0.314 AC XY: 23255 AN XY: 74154

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.233

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.0789

Gnomad4 SAS AF: 0.376

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.323

Alfa AF: 0.318 Hom.: 984

Bravo AF: 0.305

Asia WGS AF: 0.240 AC: 827 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.21
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1355459; hg19: chr6-23871700; COSMIC: COSV69193792;