rs870614

Variant names:

• chr16-85950409-G-A
• rs870614

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 0.258 in 152,094 control chromosomes in the GnomAD database, including 5,579 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 0.26 (5579 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.129

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39172 AN: 151976 Hom.: 5564 Cov.: 32

Gnomad AFR AF: 0.367

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.337

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.258 AC: 39217 AN: 152094 Hom.: 5579 Cov.: 32 AF XY: 0.253 AC XY: 18782 AN XY: 74374

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.337

Gnomad4 EAS AF: 0.174

Gnomad4 SAS AF: 0.278

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.276

Alfa AF: 0.247 Hom.: 1079

Bravo AF: 0.271

Asia WGS AF: 0.233 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs870614; hg19: chr16-85984015;