rs16848653

chr2-163578899-T-Cchr2-163578899-T-G

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 0.106 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.105 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

Gnomad4 AFR AF: 0.151

Gnomad4 AMR AF: 0.0756

Gnomad4 ASJ AF: 0.0884

Gnomad4 EAS AF: 0.232

Gnomad4 SAS AF: 0.148

Gnomad4 FIN AF: 0.0672

Gnomad4 NFE AF: 0.0796

Gnomad4 OTH AF: 0.102

Alfa AF: 0.101 Hom.: 177

Bravo AF: 0.106

Asia WGS AF: 0.184 AC: 639 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	0.80
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: rs16848653; hg19: chr2-164435409;