rs1488318

Positions:

• chr6-93973885-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 0.466 in 152,032 control chromosomes in the GnomAD database, including 17,500 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 0.47 (17500 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.336

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 (SAS) allele frequency at 95% confidence interval = 0.65 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: 0.466 AC: 70747 AN: 151912 Hom.: 17477 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.364

Gnomad AMR AF: 0.497

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.490

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.466 AC: 70818 AN: 152032 Hom.: 17500 Cov.: 32 AF XY: 0.470 AC XY: 34908 AN XY: 74284

Gnomad4 AFR AF: 0.303

Gnomad4 AMR AF: 0.497

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.633

Gnomad4 SAS AF: 0.669

Gnomad4 FIN AF: 0.490

Gnomad4 NFE AF: 0.531

Gnomad4 OTH AF: 0.452

Alfa AF: 0.496 Hom.: 6696

Bravo AF: 0.451

Asia WGS AF: 0.627 AC: 2181 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	0.18
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: rs1488318; hg19: chr6-94683603;