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. The variant received -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
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.378 AC: 13594 AN: 35938

American (AMR) AF: 0.493 AC: 6383 AN: 12954

Ashkenazi Jewish (ASJ) AF: 0.529 AC: 1815 AN: 3428

East Asian (EAS) AF: 0.315 AC: 1405 AN: 4464

South Asian (SAS) AF: 0.627 AC: 2688 AN: 4288

European-Finnish (FIN) AF: 0.383 AC: 2848 AN: 7430

Middle Eastern (MID) AF: 0.635 AC: 160 AN: 252

European-Non Finnish (NFE) AF: 0.467 AC: 30740 AN: 65768

Other (OTH) AF: 0.486 AC: 929 AN: 1912

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.5
DANN	Benign	0.69
PhyloP100		-0.52

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7565213;

hg19: chr2-204743409;