rs7565213

Variant names:

• chr2-203878686-G-A
• rs7565213

Your query was ambiguous. Multiple possible variants found:

• chr2-203878686-G-A
• chr2-203878686-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;