rs7565213

chr2-203878686-G-Achr2-203878686-G-C

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 0.444 in 137,312 control chromosomes in the GnomAD database, including 13,401 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 0.44 (13401 hom., cov: 20)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.607 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: 0.444 AC: 60917 AN: 137248 Hom.: 13400 Cov.: 20

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.529

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.467

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.444 AC: 60937 AN: 137312 Hom.: 13401 Cov.: 20 AF XY: 0.445 AC XY: 29052 AN XY: 65348

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.529

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.627

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.467

Gnomad4 OTH AF: 0.486

Alfa AF: 0.433 Hom.: 1811

Bravo AF: 0.425

Asia WGS AF: 0.480 AC: 1671 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.5
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7565213; hg19: chr2-204743409;