chr2-163578899-T-C

Variant names:

• chr2-163578899-T-C
• rs16848653

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;