chr2-102296204-C-A

Position:

• chr2-102296204-C-A

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 0.164 in 151,740 control chromosomes in the GnomAD database, including 2,729 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 0.16 (2729 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24861 AN: 151622 Hom.: 2717 Cov.: 31

Gnomad AFR AF: 0.0774

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.207

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.164 AC: 24880 AN: 151740 Hom.: 2729 Cov.: 31 AF XY: 0.173 AC XY: 12792 AN XY: 74150

Gnomad4 AFR AF: 0.0772

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.244

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.207

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.162

Alfa AF: 0.155 Hom.: 1509

Bravo AF: 0.169

Asia WGS AF: 0.298 AC: 1036 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.63
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: rs951774; hg19: chr2-102912664;