rs17210989

Variant names:

• chr16-55139182-G-A
• rs17210989

Your query was ambiguous. Multiple possible variants found:

• chr16-55139182-G-A
• chr16-55139182-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 0.0468 in 152,314 control chromosomes in the GnomAD database, including 220 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 0.047 (220 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.563

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0981 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: 0.0467 AC: 7115 AN: 152196 Hom.: 221 Cov.: 33

Gnomad AFR AF: 0.0290

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0214

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.00482

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.0691

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0604

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0468 AC: 7123 AN: 152314 Hom.: 220 Cov.: 33 AF XY: 0.0462 AC XY: 3439 AN XY: 74480

Gnomad4 AFR AF: 0.0290

Gnomad4 AMR AF: 0.0214

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.00484

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0691

Gnomad4 NFE AF: 0.0604

Gnomad4 OTH AF: 0.0430

Alfa AF: 0.0525 Hom.: 309

Bravo AF: 0.0401

Asia WGS AF: 0.0510 AC: 177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17210989; hg19: chr16-55173094;