rs16858841

chr2-218167540-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0234 in 152,280 control chromosomes in the GnomAD database, including 49 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 0.023 (49 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.445

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0234 (3556/152280) while in subpopulation NFE AF= 0.0315 (2140/68004). AF 95% confidence interval is 0.0304. There are 49 homozygotes in gnomad4. There are 1740 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 49 gene

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: 0.0234 AC: 3557 AN: 152162 Hom.: 49 Cov.: 32

Gnomad AFR AF: 0.00563

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0200

Gnomad ASJ AF: 0.0648

Gnomad EAS AF: 0.0252

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0261

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0315

Gnomad OTH AF: 0.0296

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

GnomAD4 genome AF: 0.0234 AC: 3556 AN: 152280 Hom.: 49 Cov.: 32 AF XY: 0.0234 AC XY: 1740 AN XY: 74464

Gnomad4 AFR AF: 0.00561

Gnomad4 AMR AF: 0.0200

Gnomad4 ASJ AF: 0.0648

Gnomad4 EAS AF: 0.0255

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.0261

Gnomad4 NFE AF: 0.0315

Gnomad4 OTH AF: 0.0289

Alfa AF: 0.0244 Hom.: 6

Bravo AF: 0.0217

Asia WGS AF: 0.0480 AC: 167 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.58
Dann	Benign	0.30

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16858841; hg19: chr2-219032263;