rs2161510

Positions:

• chr16-15217755-T-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 0.55 in 146,850 control chromosomes in the GnomAD database, including 23,188 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 0.55 (23188 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.649 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: 0.551 AC: 80787 AN: 146734 Hom.: 23170 Cov.: 23

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.675

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.600

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

GnomAD4 genome AF: 0.550 AC: 80839 AN: 146850 Hom.: 23188 Cov.: 23 AF XY: 0.546 AC XY: 39010 AN XY: 71454

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.675

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.595

Alfa AF: 0.596 Hom.: 2942

Bravo AF: 0.559

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0030
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: rs2161510; hg19: chr16-15311612;