rs16848653

Variant names:

• chr2-163578899-T-C
• rs16848653

Your query was ambiguous. Multiple possible variants found:

• chr2-163578899-T-C
• chr2-163578899-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.106 in 152,222 control chromosomes in the GnomAD database, including 990 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 0.11 (990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.801
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.105 AC: 16037 AN: 152104 Hom.: 989 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.0884

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.148

Gnomad FIN AF: 0.0672

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0796

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.106 AC: 16064 AN: 152222 Hom.: 990 Cov.: 32 AF XY: 0.106 AC XY: 7858 AN XY: 74436

African (AFR) AF: 0.151 AC: 6274 AN: 41538

American (AMR) AF: 0.0756 AC: 1155 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0884 AC: 307 AN: 3472

East Asian (EAS) AF: 0.232 AC: 1196 AN: 5164

South Asian (SAS) AF: 0.148 AC: 713 AN: 4822

European-Finnish (FIN) AF: 0.0672 AC: 713 AN: 10606

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0796 AC: 5413 AN: 68016

Other (OTH) AF: 0.102 AC: 215 AN: 2112

Alfa AF: 0.0951 Hom.: 1233

Bravo AF: 0.106

Asia WGS AF: 0.184 AC: 639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.80
DANN	Benign	0.54
PhyloP100		-0.80

Splicing

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

Other links and lift over

dbSNP: rs16848653; hg19: chr2-164435409;