rs2056634

Variant names:

• chr2-7243106-T-C
• rs2056634

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 0.146 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
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• 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

African (AFR) AF: 0.0389 AC: 1618 AN: 41560

American (AMR) AF: 0.190 AC: 2908 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3470

East Asian (EAS) AF: 0.0452 AC: 234 AN: 5180

South Asian (SAS) AF: 0.123 AC: 594 AN: 4820

European-Finnish (FIN) AF: 0.131 AC: 1392 AN: 10598

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.211 AC: 14331 AN: 68000

Other (OTH) AF: 0.156 AC: 331 AN: 2116

Alfa AF: 0.191 Hom.: 1567

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
PhyloP100		0.15

Splicing

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

Other links and lift over

dbSNP: rs2056634; hg19: chr2-7383237;