rs16864170

Variant names:

• chr2-5767748-T-C
• rs16864170

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 0.0389 in 152,288 control chromosomes in the GnomAD database, including 170 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 0.039 (170 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.132

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 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: 0.0389 AC: 5920 AN: 152170 Hom.: 172 Cov.: 33

Gnomad AFR AF: 0.0231

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.0298

Gnomad ASJ AF: 0.0343

Gnomad EAS AF: 0.00250

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0451

Gnomad OTH AF: 0.0482

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

GnomAD4 genome AF: 0.0389 AC: 5918 AN: 152288 Hom.: 170 Cov.: 33 AF XY: 0.0410 AC XY: 3050 AN XY: 74480

Gnomad4 AFR AF: 0.0233

Gnomad4 AMR AF: 0.0298

Gnomad4 ASJ AF: 0.0343

Gnomad4 EAS AF: 0.00251

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.0418

Gnomad4 NFE AF: 0.0451

Gnomad4 OTH AF: 0.0468

Alfa AF: 0.0426 Hom.: 168

Bravo AF: 0.0339

Asia WGS AF: 0.0520 AC: 181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16864170; hg19: chr2-5907880;