rs16858841

Variant names:

• chr2-218167540-G-A
• rs16858841

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 49 gene

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: 0.0234 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

African (AFR) AF: 0.00561 AC: 233 AN: 41544

American (AMR) AF: 0.0200 AC: 306 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0648 AC: 225 AN: 3470

East Asian (EAS) AF: 0.0255 AC: 132 AN: 5186

South Asian (SAS) AF: 0.0284 AC: 137 AN: 4826

European-Finnish (FIN) AF: 0.0261 AC: 277 AN: 10624

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0315 AC: 2140 AN: 68004

Other (OTH) AF: 0.0289 AC: 61 AN: 2114

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
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs16858841; hg19: chr2-219032263;