rs870614

Variant names:

• chr16-85950409-G-A
• rs870614

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.368 AC: 15232 AN: 41434

American (AMR) AF: 0.224 AC: 3429 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.337 AC: 1171 AN: 3470

East Asian (EAS) AF: 0.174 AC: 902 AN: 5172

South Asian (SAS) AF: 0.278 AC: 1341 AN: 4820

European-Finnish (FIN) AF: 0.105 AC: 1115 AN: 10606

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.221 AC: 15050 AN: 67992

Other (OTH) AF: 0.276 AC: 582 AN: 2110

Alfa AF: 0.245 Hom.: 1704

Bravo AF: 0.271

Asia WGS AF: 0.233 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.54
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs870614; hg19: chr16-85984015;