rs1592410

chr6-29516191-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 0.452 in 151,996 control chromosomes in the GnomAD database, including 15,815 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 0.45 (15815 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.503 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: 0.452 AC: 68630 AN: 151878 Hom.: 15772 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.452 AC: 68714 AN: 151996 Hom.: 15815 Cov.: 32 AF XY: 0.451 AC XY: 33504 AN XY: 74290

Gnomad4 AFR AF: 0.509

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.517

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.430

Alfa AF: 0.435 Hom.: 19152

Bravo AF: 0.439

Asia WGS AF: 0.505 AC: 1755 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	6.5
Dann	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1592410; hg19: chr6-29483968;