rs2056634

Variant names:

• chr2-7243106-T-C
• rs2056634

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 0.146 in 152,234 control chromosomes in the GnomAD database, including 2,065 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 0.15 (2065 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.152

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.208 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: 0.146 AC: 22213 AN: 152116 Hom.: 2070 Cov.: 32

Gnomad AFR AF: 0.0390

Gnomad AMI AF: 0.237

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0455

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.211

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.146 AC: 22203 AN: 152234 Hom.: 2065 Cov.: 32 AF XY: 0.143 AC XY: 10632 AN XY: 74444

Gnomad4 AFR AF: 0.0389

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.0452

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.131

Gnomad4 NFE AF: 0.211

Gnomad4 OTH AF: 0.156

Alfa AF: 0.190 Hom.: 1402

Bravo AF: 0.147

Asia WGS AF: 0.100 AC: 349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2056634; hg19: chr2-7383237;