rs1870046

chr8-94232307-G-C

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 0.39 in 152,080 control chromosomes in the GnomAD database, including 13,156 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 0.39 (13156 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.209

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 = 0.504 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: 0.390 AC: 59326 AN: 151962 Hom.: 13158 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.640

Gnomad AMR AF: 0.336

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.469

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.390 AC: 59343 AN: 152080 Hom.: 13156 Cov.: 32 AF XY: 0.389 AC XY: 28931 AN XY: 74330

Gnomad4 AFR AF: 0.179

Gnomad4 AMR AF: 0.335

Gnomad4 ASJ AF: 0.476

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.469

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.431

Alfa AF: 0.436 Hom.: 1936

Bravo AF: 0.367

Asia WGS AF: 0.394 AC: 1371 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	1.6
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1870046; hg19: chr8-95244535;