rs1555082

chr6-21346942-C-T

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 0.464 in 151,950 control chromosomes in the GnomAD database, including 19,438 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 0.46 (19438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.263

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.599 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: 0.465 AC: 70561 AN: 151832 Hom.: 19441 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.590

Gnomad AMR AF: 0.601

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.332

Gnomad SAS AF: 0.484

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.464 AC: 70565 AN: 151950 Hom.: 19438 Cov.: 32 AF XY: 0.467 AC XY: 34671 AN XY: 74248

Gnomad4 AFR AF: 0.154

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.571

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.487

Gnomad4 FIN AF: 0.591

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.499

Alfa AF: 0.546 Hom.: 3384

Bravo AF: 0.447

Asia WGS AF: 0.391 AC: 1361 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.7
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555082; hg19: chr6-21347173;